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Removing extended event related unit tests

This commit is contained in:
Eric Banks 2012-04-02 14:40:36 -04:00
parent 99d27ddcc4
commit 326220c91c
1 changed files with 1 additions and 173 deletions
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174
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
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@ -43,49 +43,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
} }
@Test
public void testIndelBaseQualityFiltering() {
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
before.setReadBases(bases);
before.setBaseQualities(new byte[] {20,20,20,20,0,20,20,20,20,20});
before.setCigarString("10M");
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,2,10);
during.setReadBases(bases);
during.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20,20});
during.setCigarString("4M1I6M");
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header,"after",0,3,10);
after.setReadBases(bases);
after.setBaseQualities(new byte[] {20,20,0,20,20,20,20,20,20,20});
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 foundExtendedEventPileup = false;
while (li.hasNext()) {
AlignmentContext context = li.next();
if(!context.hasExtendedEventPileup())
continue;
ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup().getBaseFilteredPileup(10);
Assert.assertEquals(pileup.getLocation().getStart(), 5, "Extended event pileup at wrong location");
Assert.assertEquals(pileup.getNumberOfElements(), 3, "Pileup size is incorrect");
foundExtendedEventPileup = true;
}
Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
}
@Test @Test
public void testIndelsInRegularPileup() { public void testIndelsInRegularPileup() {
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
@ -93,7 +50,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
// create a test version of the Reads object // create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties(); ReadProperties readAttributes = createTestReadProperties();
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10); SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
before.setReadBases(bases); before.setReadBases(bases);
@ -136,59 +92,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
Assert.assertTrue(foundIndel,"Indel in pileup not found"); Assert.assertTrue(foundIndel,"Indel in pileup not found");
} }
/**
* Right now, the GATK's extended event pileup DOES NOT include reads which stop immediately before an insertion
* but DOES include reads which stop immediately after an insertion. This is almost certainly WRONG. Eric is
* figuring out the right way to handle this; in the meantime, adding this test to monitor that:
* A) the behavior is consistent
* B) so that we do end up with an automated test for this case when the model is fixed.
*/
@Test
public void testIndelPileupContainsAbuttingReads() {
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
final byte[] quals = new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20};
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
before.setReadBases(bases);
before.setBaseQualities(quals);
before.setCigarString("10M");
SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,6,10);
during.setReadBases(bases);
during.setBaseQualities(quals);
during.setCigarString("5M1I5M");
SAMRecord after = ArtificialSAMUtils.createArtificialRead(header,"after",0,11,10);
after.setReadBases(bases);
after.setBaseQualities(quals);
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 foundExtendedEventPileup = false;
while (li.hasNext()) {
AlignmentContext context = li.next();
if(!context.hasExtendedEventPileup())
continue;
Assert.assertEquals(context.getLocation().getStart(), 10, "Extended event pileup at wrong location");
Assert.assertEquals(context.size(), 2, "Pileup size is incorrect");
Assert.assertEquals(context.getExtendedEventPileup().getReads().get(0), during, "Read in pileup is incorrect");
Assert.assertEquals(context.getExtendedEventPileup().getReads().get(1), after, "Read in pileup is incorrect");
foundExtendedEventPileup = true;
}
Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
}
@Test @Test
public void testWholeIndelReadInIsolation() { public void testWholeIndelReadInIsolation() {
final int firstLocus = 44367789; final int firstLocus = 44367789;
@ -214,17 +117,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
ReadBackedPileup basePileup = alignmentContext.getBasePileup(); ReadBackedPileup basePileup = alignmentContext.getBasePileup();
Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size"); Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
Assert.assertSame(basePileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect"); Assert.assertSame(basePileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
// Turn on extended events, and make sure the event is found.
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
li = makeLTBS(reads, readAttributes);
Assert.assertTrue(li.hasNext(),"LocusIteratorByState with extended events should contain exactly one pileup");
alignmentContext = li.next();
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus-1,"Extended event pileup is at incorrect location.");
ReadBackedExtendedEventPileup extendedEventPileup = alignmentContext.getExtendedEventPileup();
Assert.assertEquals(extendedEventPileup.getReads().size(),1,"Pileup is of incorrect size");
Assert.assertSame(extendedEventPileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
} }
/** /**
@ -232,7 +124,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
* not negatively influence the ordering of the pileup. * not negatively influence the ordering of the pileup.
*/ */
@Test @Test
public void testWholeIndelReadWithoutExtendedEvents() { public void testWholeIndelRead() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1; final int firstLocus = 44367788, secondLocus = firstLocus + 1;
SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76); SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76);
@ -280,70 +172,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
Assert.assertEquals(numAlignmentContextsFound,2,"Found incorrect number of alignment contexts"); Assert.assertEquals(numAlignmentContextsFound,2,"Found incorrect number of alignment contexts");
} }
/**
* 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 testWholeIndelReadWithExtendedEvents() {
final int firstLocus = 44367788, secondLocus = firstLocus + 1;
// create a test version of the Reads object
ReadProperties readAttributes = createTestReadProperties();
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
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,1);
fullMatchAfterIndel.setReadBases(Utils.dupBytes((byte)'A',1));
fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte)'@',1));
fullMatchAfterIndel.setCigarString("1M");
List<SAMRecord> reads = Arrays.asList(leadingRead,indelOnlyRead,fullMatchAfterIndel);
// create the iterator by state with the fake reads and fake records
li = makeLTBS(reads,readAttributes);
Assert.assertTrue(li.hasNext(),"Missing first locus at " + firstLocus);
AlignmentContext alignmentContext = li.next();
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect locus at this position; should be " + firstLocus);
List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(readsAtLocus.size(),1,"Wrong number of reads at locus " + firstLocus);
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at locus " + firstLocus);
Assert.assertTrue(li.hasNext(),"Missing extended event at " + firstLocus);
alignmentContext = li.next();
Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect extended event locus at this position; should be " + firstLocus);
readsAtLocus = alignmentContext.getExtendedEventPileup().getReads();
Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + firstLocus);
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + firstLocus);
Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + firstLocus);
// Weird, but as above, reads immediately after the indel are included in the extended event pileup
Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + firstLocus);
// 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(),"Missing base pileup at " + secondLocus);
alignmentContext = li.next();
Assert.assertEquals(alignmentContext.getLocation().getStart(),secondLocus,"Incorrect extended event locus at this position; should be " + secondLocus);
readsAtLocus = alignmentContext.getBasePileup().getReads();
Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + secondLocus);
Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + secondLocus);
Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + secondLocus);
// Weird, but as above, reads immediately after the indel are included in the extended event pileup
Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + secondLocus);
Assert.assertFalse(li.hasNext(),"Too many alignment contexts");
}
private static ReadProperties createTestReadProperties() { private static ReadProperties createTestReadProperties() {
return new ReadProperties( return new ReadProperties(
Collections.<SAMReaderID>emptyList(), Collections.<SAMReaderID>emptyList(),