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a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.

This commit is contained in:
Guillermo del Angel 2012-02-25 13:57:28 -05:00
parent c9a4c74f7a
commit dea35943d1
2 changed files with 56 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -465,7 +465,7 @@ public class LocusIteratorByState extends LocusIterator {
final CigarElement nextElement = state.peekForwardOnGenome(); // next cigar element
final CigarOperator nextOp = nextElement.getOperator();
final int readOffset = state.getReadOffset(); // the base offset on this read
byte[] insertedBases = Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + nextElement.getLength());
int nextElementLength = nextElement.getLength();
if (op == CigarOperator.N) // N's are never added to any pileup
@ -483,8 +483,12 @@ public class LocusIteratorByState extends LocusIterator {
}
else {
if (!filterBaseInRead(read, location.getStart())) {
String insertedBaseString = null;
if (nextOp == CigarOperator.I) {
insertedBaseString = new String(Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + nextElement.getLength()));
}
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart()),
new String(insertedBases),nextElementLength));
insertedBaseString,nextElementLength));
size++;
if (read.getMappingQuality() == 0)
nMQ0Reads++;

50
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
View File

@ -6,6 +6,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
@ -85,6 +86,55 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
}
@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();
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[] {20,20,20,20,20,20,20,20,20,20});
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();
if(!context.hasBasePileup())
continue;
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");
}
/**
* Right now, the GATK's extended event pileup DOES NOT include reads which stop immediately before an insertion