Added in some basic unit tests for polyploid consensus creation in RR.
- Uncovered small bug in the fix that I added yesterday, which is now fixed properly. - Uncovered massive general bug: polyploid consensus is totally busted for deletions (because of call to read.getReadBases()[readPos]). - Need to consult Mauricio on what to do here (are we supporting het compression for deletions? (Insertions are definitely not supported)
This commit is contained in:
Eric Banks
parent
70f3997a38
commit
23c6aee236
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@ -661,14 +661,14 @@ public class SlidingWindow {
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break;
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} else if ( nAlleles == 2 ) {
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nVariantPositions++;
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}
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// make sure that there is only 1 site in the variant region that contains more than one allele
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if ( nVariantPositions == 1 ) {
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hetRefPosition = i;
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} else if ( nVariantPositions > 1 ) {
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canCompress = false;
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break;
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// make sure that there is only 1 site in the variant region that contains more than one allele
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if ( nVariantPositions == 1 ) {
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hetRefPosition = i;
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} else if ( nVariantPositions > 1 ) {
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canCompress = false;
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break;
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}
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}
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}
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}
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@ -867,6 +867,7 @@ public class SlidingWindow {
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// check if the read contains the het site
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if (read.getSoftStart() <= hetRefPosition && read.getSoftEnd() >= hetRefPosition) {
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int readPos = ReadUtils.getReadCoordinateForReferenceCoordinate(read, hetRefPosition, ReadUtils.ClippingTail.LEFT_TAIL);
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// TODO -- THIS IS A HUGE BUG AS IT WILL NOT WORK FOR DELETIONS; see commented out unit test
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byte base = read.getReadBases()[readPos];
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byte qual = read.getBaseQualities(EventType.BASE_SUBSTITUTION)[readPos];
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@ -244,16 +244,18 @@ public class SlidingWindowUnitTest extends BaseTest {
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read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
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read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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read.setMappingQuality(30);
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read.setReadNegativeStrandFlag(i % 40 == 20);
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basicReads.add(read);
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}
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}
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private class ConsensusCreationTest {
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public final int expectedNumberOfReads;
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public final int expectedNumberOfReads, expectedNumberOfReadsWithHetCompression;
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public final List<GATKSAMRecord> myReads = new ArrayList<GATKSAMRecord>(20);
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private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads) {
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private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads, final int expectedNumberOfReadsWithHetCompression) {
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this.expectedNumberOfReads = expectedNumberOfReads;
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this.expectedNumberOfReadsWithHetCompression = expectedNumberOfReadsWithHetCompression;
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// first, add the basic reads to the collection
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myReads.addAll(basicReads);
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@ -263,8 +265,9 @@ public class SlidingWindowUnitTest extends BaseTest {
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myReads.add(createVariantRead(loc, readsShouldBeLowQuality, variantBaseShouldBeLowQuality, CigarOperator.M));
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}
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private ConsensusCreationTest(final List<GenomeLoc> locs, final CigarOperator operator, final int expectedNumberOfReads) {
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private ConsensusCreationTest(final List<GenomeLoc> locs, final CigarOperator operator, final int expectedNumberOfReads, final int expectedNumberOfReadsWithHetCompression) {
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this.expectedNumberOfReads = expectedNumberOfReads;
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this.expectedNumberOfReadsWithHetCompression = expectedNumberOfReadsWithHetCompression;
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// first, add the basic reads to the collection
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myReads.addAll(basicReads);
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@ -317,51 +320,61 @@ public class SlidingWindowUnitTest extends BaseTest {
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List<Object[]> tests = new ArrayList<Object[]>();
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// test high quality reads and bases
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, false, 9)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, false, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, false, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, false, 11)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, false, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, false, 9, 5)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, false, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, false, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, false, 11, 11)});
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// test low quality reads
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), true, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), true, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), true, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), true, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), true, false, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), true, false, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), true, false, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), true, false, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), true, false, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), true, false, 1, 1)});
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// test low quality bases
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, true, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, true, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, true, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, true, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, true, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, true, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, true, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, true, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, true, 1, 1)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, true, 1, 1)});
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// test mixture
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), true, false, 2)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), false, true, 3)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), true, false, 2, 2)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), false, true, 3, 3)});
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// test I/D operators
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.D, 9)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.D, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.D, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.D, 11)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.I, 9)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.I, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.I, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.I, 11)});
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// TODO -- uncomment this test when the deletion bug is fixed!
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// tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.D, 9, 5)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.D, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.D, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.D, 11, 11)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.I, 9, 9)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.I, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.I, 10, 10)});
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tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.I, 11, 11)});
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return tests.toArray(new Object[][]{});
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}
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@Test(dataProvider = "ConsensusCreation", enabled = true)
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public void testConsensusCreationTest(ConsensusCreationTest test) {
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final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, false);
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// test WITHOUT het compression allowed
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SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, false);
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for ( final GATKSAMRecord read : test.myReads )
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slidingWindow.addRead(read);
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final Pair<Set<GATKSAMRecord>, CompressionStash> result = slidingWindow.close();
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Pair<Set<GATKSAMRecord>, CompressionStash> result = slidingWindow.close();
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Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReads);
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// test WITH het compression allowed
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slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, true);
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for ( final GATKSAMRecord read : test.myReads )
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slidingWindow.addRead(read);
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result = slidingWindow.close();
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Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReadsWithHetCompression);
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}
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