@BeforeTest
public void setUp() {
builder.setReadLength(READ_LENGTH);
// Will be kept when an interval overlaps chromosome 1 in the first 151
// bases.
builder.addPair("mapped_pair_chr1", 0, 1, 151);
// Will be kept when an interval overlaps chromsome 2 in the first 151
// bases.
builder.addPair("mapped_pair_chr2", 1, 1, 151);
// The first read should pass and second should not, but both will
// be kept in first test.
builder.addPair("one_of_pair", 0, 1, 1000);
// The second read is unmapped, but both should be kept in an
// interval test where the interval includes chromosome four, where
// read one will overlap.
builder.addPair(
"second_mate_unmapped",
3,
-1,
1,
1000,
false,
true,
"151M",
null,
false,
false,
false,
false,
-1);
// The first read is unmapped but both should be kept in an
// interval test where the interval includes chromosome four, where
// read two will overlap.
builder.addPair(
"first_mate_unmapped",
-1,
3,
1000,
1,
true,
false,
null,
"151M",
false,
false,
false,
false,
-1);
// This pair will overlap any interval that includes chromosome 1:1000
builder.addPair("prove_one_of_pair", 0, 1000, 1000);
// These reads are unmapped and will not map to any intervals, so they
// are never kept. This is tested below.
builder.addPair(
"both_unmapped", -1, -1, 1, 1, true, true, null, null, false, false, false, false, -1);
// Secondary alignments are never kept by the interval filter.
builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, true, false);
// Supplementary alignment are never kept by the interval filter.
builder.addFrag("mapped_pair_chr1", 0, 1, false, false, "151M", null, -1, false, true);
}
/**
* Basic positive and negative tests for the FailsReadQualityFilter
*
* @param readQualityFlag The read quality flag to be tested
* @param expectedResult The expected result (true is the sequence should match the filter,
* otherwise false)
*/
@Test(dataProvider = "data")
public void testFailsReadQualityFilter(
final String testName, final boolean readQualityFlag, final boolean expectedResult) {
builder.addUnmappedFragment("testfrag");
final SAMRecord record = builder.iterator().next();
record.setReadFailsVendorQualityCheckFlag(readQualityFlag);
Assert.assertEquals(filter.filterOut(record), expectedResult, testName);
}
@Test(dataProvider = "testData")
public void testIntervalPairFilter(
final List<Interval> intervals, final long expectedPassingRecords) {
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervals);
long actualPassingRecords =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.count();
Assert.assertEquals(actualPassingRecords, expectedPassingRecords);
}
/////////////////////////////////////////////////////////////////////////////
// Used to generate the Sam Record Sets with SamRecordSetBuilder.addPair().
// testNumber 1: runGcBiasMultiLevelTest, generates records aligning to chrM and chrO
// testNumber 2: runWindowsComparisonTest, generates records aligning to chrM,N,O.
/////////////////////////////////////////////////////////////////////////////
public void setupTest1(
final int ID,
final String readGroupId,
final SAMReadGroupRecord readGroupRecord,
final String sample,
final String library,
final SAMFileHeader header,
final SAMRecordSetBuilder setBuilder)
throws IOException {
final String separator = ":";
final int contig1 = 0;
final int contig2 = 1;
readGroupRecord.setSample(sample);
readGroupRecord.setPlatform(platform);
readGroupRecord.setLibrary(library);
readGroupRecord.setPlatformUnit(readGroupId);
header.addReadGroup(readGroupRecord);
setBuilder.setReadGroup(readGroupRecord);
setBuilder.setUseNmFlag(true);
setBuilder.setHeader(header);
final int max = 800;
final int min = 1;
final Random rg = new Random(5);
// add records that align to chrM and O but not N
for (int i = 0; i < NUM_READS; i++) {
final int start = rg.nextInt(max) + min;
final String newReadName = READ_NAME + separator + ID + separator + i;
if (i != NUM_READS - 1) {
setBuilder.addPair(newReadName, contig1, start + ID, start + ID + LENGTH);
} else {
setBuilder.addPair(newReadName, contig2, start + ID, start + ID + LENGTH);
}
}
}
@Test
public void testNotPrimaryReads() {
final List<Interval> intervalList = new ArrayList<>();
final Interval interval1 = new Interval("chr1", 1, 999);
intervalList.add(interval1);
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList);
boolean notPrimary =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.anyMatch(
rec -> rec.getNotPrimaryAlignmentFlag() || rec.getSupplementaryAlignmentFlag());
Assert.assertFalse(notPrimary);
}
@Test
public void testUnmappedPair() {
final List<Interval> intervalList = new ArrayList<>();
final Interval interval1 = new Interval("chr1", 1, 999);
final Interval interval2 = new Interval("chr3", 1, 2);
final Interval interval3 = new Interval("chr2", 1, 2);
final Interval interval4 = new Interval("chr4", 1, 2);
intervalList.addAll(CollectionUtil.makeList(interval1, interval2, interval3, interval4));
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList);
boolean unmappedPassed =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.anyMatch(rec -> rec.getReadName().equals("both_unmapped"));
Assert.assertFalse(unmappedPassed);
}