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BQSR with indels integrated! 

* added support to base before deletion in the pileup
   * refactored covariates to operate on mismatches, insertions and deletions at the same time
   * all code is in private so original BQSR is still working as usual in public
   * outputs a molten CSV with mismatches, insertions and deletions, time to play!
   * barely tested, passes my very simple tests... haven't tested edge cases.
This commit is contained in:
Mauricio Carneiro 2012-02-08 14:39:55 -05:00
parent aa097a83d5
commit 5af373a3a1
10 changed files with 37 additions and 17 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -470,7 +470,7 @@ public class LocusIteratorByState extends LocusIterator {
if (op == CigarOperator.D) {
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++;
nDeletions++;
if (read.getMappingQuality() == 0)
@ -479,7 +479,7 @@ public class LocusIteratorByState extends LocusIterator {
}
else {
if (!filterBaseInRead(read, location.getStart())) {
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++;
if (read.getMappingQuality() == 0)
nMQ0Reads++;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -39,7 +39,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
@ -212,7 +215,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
public class BAQedPileupElement extends PileupElement {
public BAQedPileupElement( final PileupElement PE ) {
super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
}
@Override

12
public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java
View File

@ -87,7 +87,7 @@ public enum NGSPlatform {
/**
* Returns the NGSPlatform corresponding to the PL tag in the read group
* @param plFromRG -- the PL field (or equivalent) in a ReadGroup object
* @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
* @return an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match
*/
public static final NGSPlatform fromReadGroupPL(final String plFromRG) {
if ( plFromRG == null ) return UNKNOWN;
@ -105,4 +105,14 @@ public enum NGSPlatform {
return UNKNOWN;
}
/**
* checks whether or not the requested platform is listed in the set (and is not unknown)
*
* @param platform the read group string that describes the platform used
* @return true if the platform is known (i.e. it's in the list and is not UNKNOWN)
*/
public static final boolean isKnown (final String platform) {
return fromReadGroupPL(platform) != UNKNOWN;
}
}

6
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -177,7 +177,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
for (int i = 0; i < reads.size(); i++) {
GATKSAMRecord read = reads.get(i);
int offset = offsets.get(i);
pileup.add(createNewPileupElement(read, offset, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
pileup.add(createNewPileupElement(read, offset, false, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
}
return pileup;
@ -196,7 +196,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
for (GATKSAMRecord read : reads) {
pileup.add(createNewPileupElement(read, offset, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
pileup.add(createNewPileupElement(read, offset, false, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
}
return pileup;
@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
// --------------------------------------------------------
//

2
public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
View File

@ -48,7 +48,7 @@ public class ExtendedEventPileupElement extends PileupElement {
public ExtendedEventPileupElement(GATKSAMRecord read, int offset, int eventLength, String eventBases, Type type) {
super(read, offset, type == Type.DELETION, false, false); // extended events are slated for removal
super(read, offset, type == Type.DELETION, false, false, false); // extended events are slated for removal
this.read = read;
this.offset = offset;
this.eventLength = eventLength;

9
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -24,6 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
protected final GATKSAMRecord read;
protected final int offset;
protected final boolean isDeletion;
protected final boolean isBeforeDeletion;
protected final boolean isBeforeInsertion;
protected final boolean isNextToSoftClip;
@ -33,6 +34,7 @@ public class PileupElement implements Comparable<PileupElement> {
* @param read the read we are adding to the pileup
* @param offset the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
* @param isDeletion whether or not this base is a deletion
* @param isBeforeDeletion whether or not this base is before a deletion
* @param isBeforeInsertion whether or not this base is before an insertion
* @param isNextToSoftClip whether or not this base is next to a soft clipped base
*/
@ -40,13 +42,14 @@ public class PileupElement implements Comparable<PileupElement> {
"read != null",
"offset >= -1",
"offset <= read.getReadLength()"})
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
if (offset < 0 && isDeletion)
throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
this.read = read;
this.offset = offset;
this.isDeletion = isDeletion;
this.isBeforeDeletion = isBeforeDeletion;
this.isBeforeInsertion = isBeforeInsertion;
this.isNextToSoftClip = isNextToSoftClip;
}
@ -55,6 +58,10 @@ public class PileupElement implements Comparable<PileupElement> {
return isDeletion;
}
public boolean isBeforeDeletion() {
return isBeforeDeletion;
}
public boolean isBeforeInsertion() {
return isBeforeInsertion;
}

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
View File

@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
}
@Override
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
}

4
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
View File

@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
}
@Override
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
return new PileupElement(read, offset, isDeletion, isBeforeDeletion, isBeforeInsertion, isNextToSoftClip);
}
}

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

@ -361,10 +361,10 @@ public class ArtificialSAMUtils {
final GATKSAMRecord left = pair.get(0);
final GATKSAMRecord right = pair.get(1);
pileupElements.add(new PileupElement(left, pos - leftStart, false, false, false));
pileupElements.add(new PileupElement(left, pos - leftStart, false, false, false, false));
if (pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd()) {
pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false));
pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false, false));
}
}

4
public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java
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@ -42,8 +42,8 @@ public class GATKSAMRecordUnitTest extends BaseTest {
@Test
public void testReducedReadPileupElement() {
PileupElement readp = new PileupElement(read, 0, false, false, false);
PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false);
PileupElement readp = new PileupElement(read, 0, false, false, false, false);
PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false, false);
Assert.assertFalse(readp.getRead().isReducedRead());