@Test public void testMap_real1() throws Exception { String key = "@2_132385096_132385222_0_1_0_0_1:0:0_1:0:0_1bfnjd/"; String val = "@2_132385096_132385222_0_1_0_0_1:0:0_1:0:0_1bfnjd//1\tS\tTAAAAAGCCGCGGCGACTAAAAGCCGCTGAGAGGGGGCAAAAAGCAGCGG\t66554410000////1.0000/----,/,.,.,,++++-----+*-****\tU\t25\t139.09267\t>2\t132512583\tF\t.\t.\t.\t18A>T\tCB_READ\t@2_132385096_132385222_0_1_0_0_1:0:0_1:0:0_1bfnjd//2\tS\tCCCCTGCCCCGCCGCGGCTTTTTGCGGCTTTCCGCCCCGGCCGCCGCGGA\t33324110000////...000//---,,...,,,++++++++++*****,\tU\t23\t135.68983\t>2\t132512814\tR\t.\t.\t.\t1G>T"; mapper.setFaix( new FaidxFileHelper("foo") { @Override public Short getKeyForChromName(String name) throws IOException { assertEquals("2", name); return (short) 0; } }); MockOutputCollector mockOutputCollector = new MockOutputCollector(); mapper.map(new Text(key), new Text(val), mockOutputCollector, null); mapper.setChromosomeFilter("2"); mapper.setStartFilter(132512600l); mapper.setEndFilter(132512800l); GenomicLocationWithQuality gl132512700 = new GenomicLocationWithQuality(); gl132512700.chromosome = 0; gl132512700.pos = 132512700; gl132512700.pMappingCorrect = -3.9301895071730983E-14; assertTrue(mockOutputCollector.keys.contains(gl132512700)); assertEquals(281, mockOutputCollector.values.get(0).insertSize); }