- Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops.
- Added RR qual correctness tests (note that this is a case where we don't add code coverage but still need to test critical infrastructure). - Also added minor cleanup of BaseUtils
This commit is contained in:
Eric Banks
parent
24ba81c062
commit
03df5e6ee6
|
|
@ -48,6 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
|
|||
|
||||
import net.sf.picard.reference.IndexedFastaSequenceFile;
|
||||
import net.sf.samtools.SAMFileHeader;
|
||||
import org.apache.commons.lang.ArrayUtils;
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
|
||||
|
|
@ -217,11 +218,13 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
return count;
|
||||
}
|
||||
|
||||
|
||||
/////////////////////////////////////////////////////////////////
|
||||
//// This section tests the consensus creation functionality ////
|
||||
/////////////////////////////////////////////////////////////////
|
||||
|
||||
private static final int readLength = 100;
|
||||
private static final int testRegionSize = 1000;
|
||||
private final List<GATKSAMRecord> basicReads = new ArrayList<GATKSAMRecord>(20);
|
||||
private IndexedFastaSequenceFile seq;
|
||||
private SAMFileHeader header;
|
||||
|
|
@ -231,7 +234,6 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
|
||||
header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
|
||||
|
||||
final int testRegionSize = 1000;
|
||||
final int readFrequency = 20;
|
||||
|
||||
basicReads.clear();
|
||||
|
|
@ -239,7 +241,7 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead" + i, 0, globalStartPosition + i, readLength);
|
||||
read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
|
||||
read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
|
||||
read.setMappingQuality((byte)30);
|
||||
read.setMappingQuality(30);
|
||||
basicReads.add(read);
|
||||
}
|
||||
}
|
||||
|
|
@ -248,7 +250,7 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
public final int expectedNumberOfReads;
|
||||
public final List<GATKSAMRecord> myReads = new ArrayList<GATKSAMRecord>(20);
|
||||
|
||||
private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final int expectedNumberOfReads) {
|
||||
private ConsensusCreationTest(final List<GenomeLoc> locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads) {
|
||||
this.expectedNumberOfReads = expectedNumberOfReads;
|
||||
|
||||
// first, add the basic reads to the collection
|
||||
|
|
@ -256,10 +258,10 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
|
||||
// then add the permuted reads
|
||||
for ( final GenomeLoc loc : locs )
|
||||
myReads.add(createVariantRead(loc, readsShouldBeLowQuality));
|
||||
myReads.add(createVariantRead(loc, readsShouldBeLowQuality, variantBaseShouldBeLowQuality));
|
||||
}
|
||||
|
||||
private GATKSAMRecord createVariantRead(final GenomeLoc loc, final boolean baseShouldBeLowQuality) {
|
||||
private GATKSAMRecord createVariantRead(final GenomeLoc loc, final boolean readShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality) {
|
||||
|
||||
final int startPos = loc.getStart() - 50;
|
||||
|
||||
|
|
@ -268,9 +270,12 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
// create a mismatch
|
||||
bases[50] = 'C';
|
||||
read.setReadBases(bases);
|
||||
final byte qual = baseShouldBeLowQuality ? (byte)10 : (byte)30;
|
||||
read.setBaseQualities(Utils.dupBytes(qual, readLength));
|
||||
read.setMappingQuality((byte)30);
|
||||
final byte[] baseQuals = Utils.dupBytes((byte) 30, readLength);
|
||||
if ( variantBaseShouldBeLowQuality )
|
||||
baseQuals[50] = (byte)10;
|
||||
read.setBaseQualities(baseQuals);
|
||||
final byte mappingQual = readShouldBeLowQuality ? (byte)10 : (byte)30;
|
||||
read.setMappingQuality(mappingQual);
|
||||
return read;
|
||||
}
|
||||
}
|
||||
|
|
@ -279,16 +284,36 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
private static final GenomeLoc loc295 = new UnvalidatingGenomeLoc("1", 0, 1000295, 1000295);
|
||||
private static final GenomeLoc loc309 = new UnvalidatingGenomeLoc("1", 0, 1000309, 1000309);
|
||||
private static final GenomeLoc loc310 = new UnvalidatingGenomeLoc("1", 0, 1000310, 1000310);
|
||||
private static final GenomeLoc loc1100 = new UnvalidatingGenomeLoc("1", 0, 1001100, 1001100);
|
||||
|
||||
@DataProvider(name = "ConsensusCreation")
|
||||
public Object[][] createConsensusCreationTestData() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(), false, 1)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290), false, 9)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, 10)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc309), false, 10)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, 11)});
|
||||
// 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(loc290), false, false, 9)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc295), false, false, 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, loc310), false, false, 11)});
|
||||
|
||||
// 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(loc290), true, false, 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, loc309), true, false, 1)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), true, false, 1)});
|
||||
|
||||
// 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(loc290), false, true, 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, loc309), false, true, 1)});
|
||||
tests.add(new Object[]{new ConsensusCreationTest(Arrays.<GenomeLoc>asList(loc290, loc310), false, true, 1)});
|
||||
|
||||
// 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), false, true, 3)});
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
|
@ -304,6 +329,110 @@ public class SlidingWindowUnitTest extends BaseTest {
|
|||
}
|
||||
|
||||
|
||||
///////////////////////////////////////////////////////////
|
||||
//// This section tests the downsampling functionality ////
|
||||
///////////////////////////////////////////////////////////
|
||||
|
||||
private class DSTest {
|
||||
public final int dcov;
|
||||
|
||||
private DSTest(final int dcov) {
|
||||
this.dcov = dcov;
|
||||
}
|
||||
}
|
||||
|
||||
@DataProvider(name = "Downsampling")
|
||||
public Object[][] createDownsamplingTestData() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
for ( int i = 1; i < basicReads.size() + 10; i++ )
|
||||
tests.add(new Object[]{new DSTest(i)});
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
@Test(dataProvider = "Downsampling", enabled = true)
|
||||
public void testDownsamplingTest(DSTest test) {
|
||||
final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, test.dcov, ReduceReads.DownsampleStrategy.Normal, false, 1, false);
|
||||
final List<GATKSAMRecord> result = slidingWindow.downsampleVariantRegion(basicReads);
|
||||
|
||||
Assert.assertEquals(result.size(), Math.min(test.dcov, basicReads.size()));
|
||||
}
|
||||
|
||||
|
||||
//////////////////////////////////////////////////////////////
|
||||
//// This section tests the consensus base quals accuracy ////
|
||||
//////////////////////////////////////////////////////////////
|
||||
|
||||
private class QualsTest {
|
||||
public final List<Integer> quals;
|
||||
public final List<GATKSAMRecord> myReads = new ArrayList<GATKSAMRecord>(5);
|
||||
|
||||
private QualsTest(final List<Integer> quals) {
|
||||
this.quals = quals;
|
||||
for ( int i = 0; i < quals.size(); i++ ) {
|
||||
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead" + i, 0, globalStartPosition, 1);
|
||||
read.setReadBases(new byte[]{(byte)'A'});
|
||||
read.setBaseQualities(new byte[]{quals.get(i).byteValue()});
|
||||
read.setMappingQuality(30);
|
||||
myReads.add(read);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@DataProvider(name = "ConsensusQuals")
|
||||
public Object[][] createConsensusQualsData() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
final int[] quals = new int[]{ 0, 5, 10, 15, 20, 30, 40, 50 };
|
||||
|
||||
for ( final int qual1 : quals ) {
|
||||
for ( final int qual2 : quals ) {
|
||||
for ( final int qual3 : quals ) {
|
||||
tests.add(new Object[]{new QualsTest(Arrays.asList(qual1, qual2, qual3))});
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
private static final byte minUsableConsensusQual = 10;
|
||||
|
||||
@Test(dataProvider = "ConsensusQuals", enabled = true)
|
||||
public void testConsensusQualsTest(QualsTest test) {
|
||||
final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, minUsableConsensusQual, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, 1, false);
|
||||
for ( final GATKSAMRecord read : test.myReads )
|
||||
slidingWindow.addRead(read);
|
||||
final Pair<Set<GATKSAMRecord>, CompressionStash> result = slidingWindow.close();
|
||||
|
||||
Assert.assertEquals(result.getFirst().size(), 1);
|
||||
final GATKSAMRecord read = result.getFirst().iterator().next();
|
||||
final int actualBaseQual = read.getReducedCount(0) * read.getBaseQualities()[0];
|
||||
final int expectedBaseQual = qualSum(test.quals);
|
||||
Assert.assertEquals(actualBaseQual, expectedBaseQual);
|
||||
}
|
||||
|
||||
private static int qualSum(final List<Integer> quals) {
|
||||
int goodBases = 0;
|
||||
int sum = 0;
|
||||
for ( final int qual : quals ) {
|
||||
if ( qual >= minUsableConsensusQual ) {
|
||||
goodBases++;
|
||||
sum += qual;
|
||||
}
|
||||
}
|
||||
|
||||
// handle a low quality consensus
|
||||
if ( sum == 0 ) {
|
||||
for ( final int qual : quals ) {
|
||||
goodBases++;
|
||||
sum += qual;
|
||||
}
|
||||
}
|
||||
|
||||
return sum - (sum % goodBases);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -38,17 +38,17 @@ import java.util.Arrays;
|
|||
public class BaseUtils {
|
||||
|
||||
public enum Base {
|
||||
A ((byte)'A'),
|
||||
C ((byte)'C'),
|
||||
G ((byte)'G'),
|
||||
T ((byte)'T'),
|
||||
N ((byte)'N'),
|
||||
D ((byte)'D');
|
||||
A ('A'),
|
||||
C ('C'),
|
||||
G ('G'),
|
||||
T ('T'),
|
||||
N ('N'),
|
||||
D ('D');
|
||||
|
||||
public byte base;
|
||||
|
||||
private Base(final byte base) {
|
||||
this.base = base;
|
||||
private Base(final char base) {
|
||||
this.base = (byte)base;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue