@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());
}
@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;
}
});
}