@Test public void testMultipleConcordantMappings() throws Exception { File testInput = new File(getClass().getResource("4f9f9_fix.txt").getFile()); String content = new Scanner(testInput).useDelimiter("\\Z").next(); String key = content.substring(0, content.indexOf("\t")); String val = content.substring(content.indexOf("\t") + 1); MockOutputCollector mockOutputCollector = new MockOutputCollector(); mapper.setAlignmentReader(new SAMAlignmentReader()); mapper.setFaix( new FaidxFileHelper("foo") { @Override public Short getKeyForChromName(String name) throws IOException { assertEquals("2", name); return (short) 9; } }); mapper.setMaxInsertSize(2500); mapper.setTargetIsize(300); mapper.setTargetIsizeSD(30); mapper.map(new Text(key), new Text(val), mockOutputCollector, null); assertEquals(9, mockOutputCollector.keys.size()); assertEquals(new HashSet(mockOutputCollector.keys).size(), mockOutputCollector.keys.size()); }