@Test
public void testMapPairedEndWithSegmentalDuplications() throws Exception {
String key = "@ERR000545.10000001 EAS139_44:1:93:532:453";
String value =
"@ERR000545.10000001 EAS139_44:1:93:532:453/1\tS\tCAAAAACCACTTGTACTCCAAAAGCTATTGAAGTTTAAGTTAAAATAAAAA\t<??>>?;<>=@?=?>8@<<9=98=:@>>>=:>>:6?7>9:?<46:;9;.:9\tR\t114\t0.00000\t>10\t43049466\tR\t.\t.\t.\t10A>C 22C>A 46-A\tCB_READ\[email protected] EAS139_44:1:93:532:453/2\tS\tTTATTGCACTTACCATGACTGTCTTCTGAAATGCATCTCAACCCTTGAATA\t;<8>>:$>=?@?>>:>=>:9=8<>1;8:<=>>9=:=7><>=;=;=>=72:>\tU\t34\t145.2313\t>10\t43039500\tF\t.\t.\t.\t3G>A";
mapper.setExclusionRegions(
new GFFFileHelper() {
@Override
public boolean doesLocationOverlap(String chrom, int start, int end) throws Exception {
if ("10".equals(chrom)
&& ((start > 43039000 && start < 43040000)
&& (end > 43039000 && end < 43040000))
|| ((start > 43049000 && start < 43050000) && (end > 43049000 && end < 43050000))) {
return true;
}
return false;
}
});
MockOutputCollector collector = new MockOutputCollector();
Reporter reporter = Mockito.mock(Reporter.class);
mapper.map(new Text(key), new Text(value), collector, reporter);
assertEquals(0, collector.keys.size());
key = "@ERR000545.10000001 EAS139_44:1:93:532:453";
value =
"@ERR000545.10000001 EAS139_44:1:93:532:453/1\tS\tCAAAAACCACTTGTACTCCAAAAGCTATTGAAGTTTAAGTTAAAATAAAAA\t<??>>?;<>=@?=?>8@<<9=98=:@>>>=:>>:6?7>9:?<46:;9;.:9\tR\t114\t0.00000\t>10\t49466\tR\t.\t.\t.\t10A>C 22C>A 46-A\tCB_READ\[email protected] EAS139_44:1:93:532:453/2\tS\tTTATTGCACTTACCATGACTGTCTTCTGAAATGCATCTCAACCCTTGAATA\t;<8>>:$>=?@?>>:>=>:9=8<>1;8:<=>>9=:=7><>=;=;=>=72:>\tU\t34\t145.2313\t>10\t39500\tF\t.\t.\t.\t3G>A";
collector = new MockOutputCollector();
mapper.map(new Text(key), new Text(value), collector, reporter);
assertEquals(101, collector.keys.size());
}
@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);
}
@Test
public void testMapPairedEnd() throws Exception {
String key = "@ERR000545.10000001 EAS139_44:1:93:532:453";
String value =
"@ERR000545.10000001 EAS139_44:1:93:532:453/1\tS\tCAAAAACCACTTGTACTCCAAAAGCTATTGAAGTTTAAGTTAAAATAAAAA\t<??>>?;<>=@?=?>8@<<9=98=:@>>>=:>>:6?7>9:?<46:;9;.:9\tR\t114\t0.00000\t>10\t43049466\tR\t.\t.\t.\t10A>C 22C>A 46-A\tCB_READ\[email protected] EAS139_44:1:93:532:453/2\tS\tTTATTGCACTTACCATGACTGTCTTCTGAAATGCATCTCAACCCTTGAATA\t;<8>>:$>=?@?>>:>=>:9=8<>1;8:<=>>9=:=7><>=;=;=>=72:>\tU\t34\t145.2313\t>10\t43039500\tF\t.\t.\t.\t3G>A";
mapper.setReadGroupId((short) 3);
MockOutputCollector collector = new MockOutputCollector();
Reporter reporter = Mockito.mock(Reporter.class);
mapper.map(new Text(key), new Text(value), collector, reporter);
int idx = 0;
for (int i = 43039500; i <= 43049500; i = i + 100) {
GenomicLocationWithQuality genomicLocationWithQuality = new GenomicLocationWithQuality();
genomicLocationWithQuality.chromosome = 9;
genomicLocationWithQuality.pos = i;
genomicLocationWithQuality.pMappingCorrect = -9.210340371976185;
assertTrue(collector.keys.contains(genomicLocationWithQuality));
assertEquals(
10017,
collector.values.get(collector.keys.indexOf(genomicLocationWithQuality)).insertSize);
assertEquals(
-9.2103,
collector.values.get(collector.keys.indexOf(genomicLocationWithQuality)).pMappingCorrect,
.0001);
assertEquals(
(short) 3,
(short)
collector.values.get(collector.keys.indexOf(genomicLocationWithQuality)).readGroupId);
idx++;
}
assertEquals(idx, collector.keys.size());
}