@Test(dataProvider = "LIBSTest")
public void testLIBS(LIBSTest params) {
final int locus = 44367788;
SAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, params.readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', params.readLength));
read.setBaseQualities(Utils.dupBytes((byte) '@', params.readLength));
read.setCigarString(params.cigar);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(Arrays.asList(read), createTestReadProperties());
final LIBS_position tester = new LIBS_position(read);
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
tester.stepForwardOnGenome();
Assert.assertEquals(pe.isBeforeDeletedBase(), tester.isBeforeDeletedBase);
Assert.assertEquals(pe.isBeforeDeletionStart(), tester.isBeforeDeletionStart);
Assert.assertEquals(pe.isAfterDeletedBase(), tester.isAfterDeletedBase);
Assert.assertEquals(pe.isAfterDeletionEnd(), tester.isAfterDeletionEnd);
Assert.assertEquals(pe.isBeforeInsertion(), tester.isBeforeInsertion);
Assert.assertEquals(pe.isAfterInsertion(), tester.isAfterInsertion);
Assert.assertEquals(pe.isNextToSoftClip(), tester.isNextToSoftClip);
Assert.assertEquals(pe.getOffset(), tester.getCurrentReadOffset());
}
}
@Test
public void testWholeIndelReadInIsolation() {
final int firstLocus = 44367789;
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord indelOnlyRead =
ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
indelOnlyRead.setCigarString("76I");
List<SAMRecord> reads = Arrays.asList(indelOnlyRead);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
// Traditionally, reads that end with indels bleed into the pileup at the following locus.
// Verify that the next pileup contains this read
// and considers it to be an indel-containing read.
Assert.assertTrue(
li.hasNext(),
"Should have found a whole-indel read in the normal base pileup without extended events enabled");
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(
alignmentContext.getLocation().getStart(),
firstLocus,
"Base pileup is at incorrect location.");
ReadBackedPileup basePileup = alignmentContext.getBasePileup();
Assert.assertEquals(basePileup.getReads().size(), 1, "Pileup is of incorrect size");
Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
}
private LegacyLocusIteratorByState makeLTBS(
List<SAMRecord> reads, ReadProperties readAttributes) {
return new LegacyLocusIteratorByState(
new FakeCloseableIterator<SAMRecord>(reads.iterator()),
readAttributes,
genomeLocParser,
LegacyLocusIteratorByState.sampleListForSAMWithoutReadGroups());
}
@Test
public void testIndelsInRegularPileup() {
final byte[] bases = new byte[] {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] indelBases =
new byte[] {'A', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'A', 'A', 'A', 'A'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header, "before", 0, 1, 10);
before.setReadBases(bases);
before.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
before.setCigarString("10M");
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header, "during", 0, 2, 10);
during.setReadBases(indelBases);
during.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
during.setCigarString("4M2I6M");
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header, "after", 0, 3, 10);
after.setReadBases(bases);
after.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
after.setCigarString("10M");
List<SAMRecord> reads = Arrays.asList(before, during, after);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
boolean foundIndel = false;
while (li.hasNext()) {
AlignmentContext context = li.next();
ReadBackedPileup pileup = context.getBasePileup().getBaseFilteredPileup(10);
for (PileupElement p : pileup) {
if (p.isBeforeInsertion()) {
foundIndel = true;
Assert.assertEquals(p.getEventLength(), 2, "Wrong event length");
Assert.assertEquals(p.getEventBases(), "CT", "Inserted bases are incorrect");
break;
}
}
}
Assert.assertTrue(foundIndel, "Indel in pileup not found");
}
/**
* Test to make sure that reads supporting only an indel (example cigar string: 76I) are
* represented properly
*/
@Test
public void testWholeIndelReadRepresentedTest() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, secondLocus, 1);
read1.setReadBases(Utils.dupBytes((byte) 'A', 1));
read1.setBaseQualities(Utils.dupBytes((byte) '@', 1));
read1.setCigarString("1I");
List<SAMRecord> reads = Arrays.asList(read1);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "A");
}
SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header, "read2", 0, secondLocus, 10);
read2.setReadBases(Utils.dupBytes((byte) 'A', 10));
read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
read2.setCigarString("10I");
reads = Arrays.asList(read2);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
ReadBackedPileup p = alignmentContext.getBasePileup();
Assert.assertTrue(p.getNumberOfElements() == 1);
PileupElement pe = p.iterator().next();
Assert.assertTrue(pe.isBeforeInsertion());
Assert.assertFalse(pe.isAfterInsertion());
Assert.assertEquals(pe.getEventBases(), "AAAAAAAAAA");
}
}
@Test
public void testXandEQOperators() {
final byte[] bases1 = new byte[] {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] bases2 = new byte[] {'A', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'A', 'C'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
SAMRecord r1 = ArtificialSAMUtils.createArtificialRead(header, "r1", 0, 1, 10);
r1.setReadBases(bases1);
r1.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r1.setCigarString("10M");
SAMRecord r2 = ArtificialSAMUtils.createArtificialRead(header, "r2", 0, 1, 10);
r2.setReadBases(bases2);
r2.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r2.setCigarString("3=1X5=1X");
SAMRecord r3 = ArtificialSAMUtils.createArtificialRead(header, "r3", 0, 1, 10);
r3.setReadBases(bases2);
r3.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r3.setCigarString("3=1X5M1X");
SAMRecord r4 = ArtificialSAMUtils.createArtificialRead(header, "r4", 0, 1, 10);
r4.setReadBases(bases2);
r4.setBaseQualities(new byte[] {20, 20, 20, 20, 20, 20, 20, 20, 20, 20});
r4.setCigarString("10M");
List<SAMRecord> reads = Arrays.asList(r1, r2, r3, r4);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, readAttributes);
while (li.hasNext()) {
AlignmentContext context = li.next();
ReadBackedPileup pileup = context.getBasePileup();
Assert.assertEquals(pileup.depthOfCoverage(), 4);
}
}
/**
* Test to make sure that reads supporting only an indel (example cigar string: 76I) do not
* negatively influence the ordering of the pileup.
*/
@Test
public void testWholeIndelRead() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord leadingRead =
ArtificialSAMUtils.createArtificialRead(header, "leading", 0, firstLocus, 76);
leadingRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
leadingRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
leadingRead.setCigarString("1M75I");
SAMRecord indelOnlyRead =
ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, secondLocus, 76);
indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
indelOnlyRead.setCigarString("76I");
SAMRecord fullMatchAfterIndel =
ArtificialSAMUtils.createArtificialRead(header, "fullMatch", 0, secondLocus, 76);
fullMatchAfterIndel.setReadBases(Utils.dupBytes((byte) 'A', 76));
fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte) '@', 76));
fullMatchAfterIndel.setCigarString("75I1M");
List<SAMRecord> reads = Arrays.asList(leadingRead, indelOnlyRead, fullMatchAfterIndel);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads, createTestReadProperties());
int currentLocus = firstLocus;
int numAlignmentContextsFound = 0;
while (li.hasNext()) {
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(
alignmentContext.getLocation().getStart(),
currentLocus,
"Current locus returned by alignment context is incorrect");
if (currentLocus == firstLocus) {
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(
readsAtLocus.size(), 1, "Wrong number of reads at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(0),
leadingRead,
"leadingRead absent from pileup at locus " + currentLocus);
} else if (currentLocus == secondLocus) {
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(
readsAtLocus.size(), 2, "Wrong number of reads at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(0),
indelOnlyRead,
"indelOnlyRead absent from pileup at locus " + currentLocus);
Assert.assertSame(
readsAtLocus.get(1),
fullMatchAfterIndel,
"fullMatchAfterIndel absent from pileup at locus " + currentLocus);
}
currentLocus++;
numAlignmentContextsFound++;
}
Assert.assertEquals(
numAlignmentContextsFound, 2, "Found incorrect number of alignment contexts");
}