@Test public void testAliases() { final SAMSequenceRecord ssr1 = new SAMSequenceRecord("1", 1); final SAMSequenceRecord ssr2 = new SAMSequenceRecord("2", 1); final SAMSequenceDictionary dict = new SAMSequenceDictionary( Arrays.asList(ssr1, ssr2)); Assert.assertEquals(dict.size(), 2); dict.addSequenceAlias("1", "chr1"); dict.addSequenceAlias("1", "01"); dict.addSequenceAlias("1", "1"); dict.addSequenceAlias("01", "chr01"); Assert.assertEquals(dict.size(), 2); Assert.assertNotNull(dict.getSequence("chr1")); Assert.assertNull(dict.getSequence("chr2")); }