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Bug fix for hard clipping reads when base insertion and base deletion qualities are present in the read. Updating HaplotypeCaller integration tests to reflect all the recent changes.

This commit is contained in:
Ryan Poplin 2012-03-05 17:54:42 -05:00
parent 14a77b1e71
commit c6ded4d23c
3 changed files with 36 additions and 14 deletions
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10
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
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@ -4,6 +4,7 @@ import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalDataManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -314,6 +315,15 @@ public class ClippingOp {
if (start == 0)
hardClippedRead.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), cigarShift.cigar));
if (read.hasBaseIndelQualities()) {
byte[] newBaseInsertionQuals = new byte[newLength];
byte[] newBaseDeletionQuals = new byte[newLength];
System.arraycopy(read.getBaseInsertionQualities(), copyStart, newBaseInsertionQuals, 0, newLength);
System.arraycopy(read.getBaseDeletionQualities(), copyStart, newBaseDeletionQuals, 0, newLength);
hardClippedRead.setBaseQualities(newBaseInsertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION);
hardClippedRead.setBaseQualities(newBaseDeletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION);
}
return hardClippedRead;
}

36
public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
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@ -151,23 +151,16 @@ public class FragmentUtils {
final int numBases = firstReadStop + secondRead.getReadLength();
final byte[] bases = new byte[numBases];
final byte[] quals = new byte[numBases];
// BUGBUG: too verbose, clean this up.
final byte[] insertionQuals = new byte[numBases];
final byte[] deletionQuals = new byte[numBases];
final byte[] firstReadBases = firstRead.getReadBases();
final byte[] firstReadQuals = firstRead.getBaseQualities();
final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();
final byte[] secondReadBases = secondRead.getReadBases();
final byte[] secondReadQuals = secondRead.getBaseQualities();
final byte[] secondReadInsertionQuals = secondRead.getBaseInsertionQualities();
final byte[] secondReadDeletionQuals = secondRead.getBaseDeletionQualities();
for(int iii = 0; iii < firstReadStop; iii++) {
bases[iii] = firstReadBases[iii];
quals[iii] = firstReadQuals[iii];
insertionQuals[iii] = firstReadInsertionQuals[iii];
deletionQuals[iii] = firstReadDeletionQuals[iii];
}
for(int iii = firstReadStop; iii < firstRead.getReadLength(); iii++) {
if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) {
@ -175,22 +168,16 @@ public class FragmentUtils {
}
bases[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadBases[iii] : secondReadBases[iii-firstReadStop] );
quals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadQuals[iii] : secondReadQuals[iii-firstReadStop] );
insertionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadInsertionQuals[iii] : secondReadInsertionQuals[iii-firstReadStop] ); // Purposefully checking the highest base quality score
deletionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadDeletionQuals[iii] : secondReadDeletionQuals[iii-firstReadStop] ); // Purposefully checking the highest base quality score
}
for(int iii = firstRead.getReadLength(); iii < numBases; iii++) {
bases[iii] = secondReadBases[iii-firstReadStop];
quals[iii] = secondReadQuals[iii-firstReadStop];
insertionQuals[iii] = secondReadInsertionQuals[iii-firstReadStop];
deletionQuals[iii] = secondReadDeletionQuals[iii-firstReadStop];
}
final GATKSAMRecord returnRead = new GATKSAMRecord(firstRead.getHeader());
returnRead.setAlignmentStart(firstRead.getUnclippedStart());
returnRead.setReadBases( bases );
returnRead.setBaseQualities( quals, RecalDataManager.BaseRecalibrationType.BASE_SUBSTITUTION );
returnRead.setBaseQualities( insertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION );
returnRead.setBaseQualities( deletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION );
returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M);
@ -199,6 +186,27 @@ public class FragmentUtils {
returnRead.setCigar( new Cigar( cList ));
returnRead.setMappingQuality( firstRead.getMappingQuality() );
if( firstRead.hasBaseIndelQualities() || secondRead.hasBaseIndelQualities() ) {
final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();
final byte[] secondReadInsertionQuals = secondRead.getBaseInsertionQualities();
final byte[] secondReadDeletionQuals = secondRead.getBaseDeletionQualities();
for(int iii = 0; iii < firstReadStop; iii++) {
insertionQuals[iii] = firstReadInsertionQuals[iii];
deletionQuals[iii] = firstReadDeletionQuals[iii];
}
for(int iii = firstReadStop; iii < firstRead.getReadLength(); iii++) {
insertionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadInsertionQuals[iii] : secondReadInsertionQuals[iii-firstReadStop] ); // Purposefully checking the highest *base* quality score
deletionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadDeletionQuals[iii] : secondReadDeletionQuals[iii-firstReadStop] ); // Purposefully checking the highest *base* quality score
}
for(int iii = firstRead.getReadLength(); iii < numBases; iii++) {
insertionQuals[iii] = secondReadInsertionQuals[iii-firstReadStop];
deletionQuals[iii] = secondReadDeletionQuals[iii-firstReadStop];
}
returnRead.setBaseQualities( insertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION );
returnRead.setBaseQualities( deletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION );
}
final ArrayList<GATKSAMRecord> returnList = new ArrayList<GATKSAMRecord>();
returnList.add(returnRead);
return returnList;

4
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -194,6 +194,10 @@ public class GATKSAMRecord extends BAMRecord {
}
}
public boolean hasBaseIndelQualities() {
return getAttribute( BQSR_BASE_INSERTION_QUALITIES ) != null || getAttribute( BQSR_BASE_DELETION_QUALITIES ) != null;
}
public byte[] getBaseInsertionQualities() {
byte[] quals = SAMUtils.fastqToPhred( getStringAttribute( BQSR_BASE_INSERTION_QUALITIES ) );
if( quals == null ) {