@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());
}
@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);
}
@Before
public void setup() {
mapper = new AlignmentsToReadPairInfoMapper();
mapper.setScorer(new ProbabilisticPairedAlignmentScorer());
mapper.setAlignmentReader(new NovoalignAlignmentReader());
mapper.setResolution(100);
mapper.setFaix(
new FaidxFileHelper("foo") {
@Override
public Short getKeyForChromName(String name) throws IOException {
assertEquals("10", name);
return (short) 9;
}
});
}