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Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int. 

For reads with high MQs (greater than max byte) the MQ was being treated as negative and failing
the min MQ filter.

Added unit test.

Delivers PT#61567540.
This commit is contained in:
Eric Banks 2013-11-27 15:53:11 -05:00
parent 42bf83cdc8
commit df6499e58c
2 changed files with 28 additions and 4 deletions
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9
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -1033,7 +1033,7 @@ public class SlidingWindow {
protected void actuallyUpdateHeaderForRead(final LinkedList<HeaderElement> header, final GATKSAMRecord read, final boolean removeRead, final int startIndex) {
final Iterator<HeaderElement> headerElementIterator = header.listIterator(startIndex);
final byte mappingQuality = (byte) read.getMappingQuality();
final int mappingQuality = read.getMappingQuality();
final boolean isNegativeStrand = read.getReadNegativeStrandFlag();
// iterator variables
@ -1062,14 +1062,15 @@ public class SlidingWindow {
break;
case D:
// deletions are added to the baseCounts with the read mapping quality as it's quality score
// deletions are added to the baseCounts with the read mapping quality as its quality score
final int nDeletionBases = cigarElement.getLength();
final byte MQbyte = mappingQuality > Byte.MAX_VALUE ? Byte.MAX_VALUE : (byte)mappingQuality;
for ( int i = 0; i < nDeletionBases; i++ ) {
headerElement = headerElementIterator.next();
if (removeRead)
headerElement.removeBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
headerElement.removeBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
else
headerElement.addBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
headerElement.addBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
}
locationIndex += nDeletionBases;
break;

23
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
View File

@ -860,6 +860,29 @@ public class SlidingWindowUnitTest extends BaseTest {
Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 0);
}
@Test
public void testUpdateHeaderForReadWithHighMQ() {
// set up the window header
final int currentHeaderStart = 100;
final LinkedList<HeaderElement> windowHeader = new LinkedList<>();
for ( int i = 0; i < readLength; i++ )
windowHeader.add(new HeaderElement(currentHeaderStart + i));
// set up the read
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, currentHeaderStart, readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
read.setMappingQuality(180);
read.setReadNegativeStrandFlag(false);
// add the read and make sure it's not filtered because of low MQ (byte vs. int)
final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 10, ReduceReads.DownsampleStrategy.Normal, false);
slidingWindow.actuallyUpdateHeaderForRead(windowHeader, read, false, 0);
for ( int i = 0; i < readLength; i++ )
Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 1);
}
//////////////////////////////////////////////////////////////////////////////////
//// This section tests functionality related to polyploid consensus creation ////
//////////////////////////////////////////////////////////////////////////////////