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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 2013-02-05 10:35:45 -05:00
parent 70f3997a38
commit 23c6aee236
2 changed files with 51 additions and 37 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -661,14 +661,14 @@ public class SlidingWindow {
break; break;
} else if ( nAlleles == 2 ) { } else if ( nAlleles == 2 ) {
nVariantPositions++; nVariantPositions++;
}
// make sure that there is only 1 site in the variant region that contains more than one allele // make sure that there is only 1 site in the variant region that contains more than one allele
if ( nVariantPositions == 1 ) { if ( nVariantPositions == 1 ) {
hetRefPosition = i; hetRefPosition = i;
} else if ( nVariantPositions > 1 ) { } else if ( nVariantPositions > 1 ) {
canCompress = false; canCompress = false;
break; break;
}
} }
} }
} }
@ -867,6 +867,7 @@ public class SlidingWindow {
// check if the read contains the het site // check if the read contains the het site
if (read.getSoftStart() <= hetRefPosition && read.getSoftEnd() >= hetRefPosition) { if (read.getSoftStart() <= hetRefPosition && read.getSoftEnd() >= hetRefPosition) {
int readPos = ReadUtils.getReadCoordinateForReferenceCoordinate(read, hetRefPosition, ReadUtils.ClippingTail.LEFT_TAIL); int readPos = ReadUtils.getReadCoordinateForReferenceCoordinate(read, hetRefPosition, ReadUtils.ClippingTail.LEFT_TAIL);
// TODO -- THIS IS A HUGE BUG AS IT WILL NOT WORK FOR DELETIONS; see commented out unit test
byte base = read.getReadBases()[readPos]; byte base = read.getReadBases()[readPos];
byte qual = read.getBaseQualities(EventType.BASE_SUBSTITUTION)[readPos]; byte qual = read.getBaseQualities(EventType.BASE_SUBSTITUTION)[readPos];

73
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
View File

@ -244,16 +244,18 @@ public class SlidingWindowUnitTest extends BaseTest {
read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setBaseQualities(Utils.dupBytes((byte)30, readLength)); read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
read.setMappingQuality(30); read.setMappingQuality(30);
read.setReadNegativeStrandFlag(i % 40 == 20);
basicReads.add(read); basicReads.add(read);
} }
} }
private class ConsensusCreationTest { private class ConsensusCreationTest {
public final int expectedNumberOfReads; public final int expectedNumberOfReads, expectedNumberOfReadsWithHetCompression;
public final List<GATKSAMRecord> myReads = new ArrayList<GATKSAMRecord>(20); public final List<GATKSAMRecord> myReads = new ArrayList<GATKSAMRecord>(20);
private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads) { private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads, final int expectedNumberOfReadsWithHetCompression) {
this.expectedNumberOfReads = expectedNumberOfReads; this.expectedNumberOfReads = expectedNumberOfReads;
this.expectedNumberOfReadsWithHetCompression = expectedNumberOfReadsWithHetCompression;
// first, add the basic reads to the collection // first, add the basic reads to the collection
myReads.addAll(basicReads); myReads.addAll(basicReads);
@ -263,8 +265,9 @@ public class SlidingWindowUnitTest extends BaseTest {
myReads.add(createVariantRead(loc, readsShouldBeLowQuality, variantBaseShouldBeLowQuality, CigarOperator.M)); myReads.add(createVariantRead(loc, readsShouldBeLowQuality, variantBaseShouldBeLowQuality, CigarOperator.M));
} }
private ConsensusCreationTest(final List<GenomeLoc> locs, final CigarOperator operator, final int expectedNumberOfReads) { private ConsensusCreationTest(final List<GenomeLoc> locs, final CigarOperator operator, final int expectedNumberOfReads, final int expectedNumberOfReadsWithHetCompression) {
this.expectedNumberOfReads = expectedNumberOfReads; this.expectedNumberOfReads = expectedNumberOfReads;
this.expectedNumberOfReadsWithHetCompression = expectedNumberOfReadsWithHetCompression;
// first, add the basic reads to the collection // first, add the basic reads to the collection
myReads.addAll(basicReads); myReads.addAll(basicReads);
@ -317,51 +320,61 @@ public class SlidingWindowUnitTest extends BaseTest {
List<Object[]> tests = new ArrayList<Object[]>(); List<Object[]> tests = new ArrayList<Object[]>();
// test high quality reads and bases // test high quality reads and bases
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, false, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, false, 9)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, false, 9, 5)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, false, 10)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, false, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, false, 10)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, false, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, false, 11)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, false, 11, 11)});
// test low quality reads // test low quality reads
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), true, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), true, false, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), true, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), true, false, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), true, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), true, false, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), true, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), true, false, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), true, false, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), true, false, 1, 1)});
// test low quality bases // test low quality bases
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, true, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, true, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, true, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, true, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, true, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, true, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, true, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, true, 1, 1)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, true, 1)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, true, 1, 1)});
// test mixture // test mixture
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), true, false, 2)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), true, false, 2, 2)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), false, true, 3)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc1100), false, true, 3, 3)});
// test I/D operators // test I/D operators
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.D, 9)}); // TODO -- uncomment this test when the deletion bug is fixed!
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.D, 10)}); // tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.D, 9, 5)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.D, 10)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.D, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.D, 11)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.D, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.I, 9)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.D, 11, 11)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.I, 10)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), CigarOperator.I, 9, 9)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.I, 10)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), CigarOperator.I, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.I, 11)}); tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), CigarOperator.I, 10, 10)});
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), CigarOperator.I, 11, 11)});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
} }
@Test(dataProvider = "ConsensusCreation", enabled = true) @Test(dataProvider = "ConsensusCreation", enabled = true)
public void testConsensusCreationTest(ConsensusCreationTest test) { public void testConsensusCreationTest(ConsensusCreationTest test) {
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); // test WITHOUT het compression allowed
SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, false);
for ( final GATKSAMRecord read : test.myReads ) for ( final GATKSAMRecord read : test.myReads )
slidingWindow.addRead(read); slidingWindow.addRead(read);
final Pair<Set<GATKSAMRecord>, CompressionStash> result = slidingWindow.close(); Pair<Set<GATKSAMRecord>, CompressionStash> result = slidingWindow.close();
Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReads); Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReads);
// test WITH het compression allowed
slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, true);
for ( final GATKSAMRecord read : test.myReads )
slidingWindow.addRead(read);
result = slidingWindow.close();
Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReadsWithHetCompression);
} }