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Added functionality in pileups to not only determine whether there's an insertion or deletion following the current position, but to also get the indel length and involved bases - definitely needed for extended event removal, and needed for pool caller indel functionality.

This commit is contained in:
Guillermo del Angel 2012-02-23 09:45:47 -05:00
parent 2c1b14d35e
commit 6866a41914
5 changed files with 50 additions and 9 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -175,8 +175,8 @@ public class LocusIteratorByState extends LocusIterator {
return String.format("%s ro=%d go=%d co=%d cec=%d %s", read.getReadName(), readOffset, genomeOffset, cigarOffset, cigarElementCounter, curElement);
}
public CigarOperator peekForwardOnGenome() {
return ( cigarElementCounter + 1 > curElement.getLength() && cigarOffset + 1 < nCigarElements ? cigar.getCigarElement(cigarOffset + 1) : curElement ).getOperator();
public CigarElement peekForwardOnGenome() {
return ( cigarElementCounter + 1 > curElement.getLength() && cigarOffset + 1 < nCigarElements ? cigar.getCigarElement(cigarOffset + 1) : curElement );
}
public CigarOperator stepForwardOnGenome() {
@ -462,15 +462,19 @@ public class LocusIteratorByState extends LocusIterator {
final SAMRecordState state = iterator.next(); // state object with the read/offset information
final GATKSAMRecord read = (GATKSAMRecord) state.getRead(); // the actual read
final CigarOperator op = state.getCurrentCigarOperator(); // current cigar operator
final CigarOperator nextOp = state.peekForwardOnGenome(); // next cigar operator
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
continue;
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.D, 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()),
null,nextOp == CigarOperator.D? nextElementLength:-1));
size++;
nDeletions++;
if (read.getMappingQuality() == 0)
@ -479,7 +483,8 @@ public class LocusIteratorByState extends LocusIterator {
}
else {
if (!filterBaseInRead(read, location.getStart())) {
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.D, 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()),
new String(insertedBases),nextElementLength));
size++;
if (read.getMappingQuality() == 0)
nMQ0Reads++;

1
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -205,6 +205,7 @@ 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 isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip, String nextEventBases, int nextEventLength );
// --------------------------------------------------------
//

2
public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
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@ -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, false); // extended events are slated for removal
super(read, offset, type == Type.DELETION, false, false, false,null,-1); // extended events are slated for removal
this.read = read;
this.offset = offset;
this.eventLength = eventLength;

31
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -27,6 +27,10 @@ public class PileupElement implements Comparable<PileupElement> {
protected final boolean isBeforeDeletion;
protected final boolean isBeforeInsertion;
protected final boolean isNextToSoftClip;
protected final int eventLength;
protected final String eventBases; // if it is a deletion, we do not have information about the actual deleted bases
// in the read itself, so we fill the string with D's; for insertions we keep actual inserted bases
/**
* Creates a new pileup element.
@ -37,12 +41,15 @@ public class PileupElement implements Comparable<PileupElement> {
* @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
* @param nextEventBases bases in event in case element comes before insertion or deletion
* @param nextEventLength length of next event in case it's insertion or deletion
*/
@Requires({
"read != null",
"offset >= -1",
"offset <= read.getReadLength()"})
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, 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,
final String nextEventBases, final int nextEventLength) {
if (offset < 0 && isDeletion)
throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
@ -52,6 +59,14 @@ public class PileupElement implements Comparable<PileupElement> {
this.isBeforeDeletion = isBeforeDeletion;
this.isBeforeInsertion = isBeforeInsertion;
this.isNextToSoftClip = isNextToSoftClip;
if (isBeforeInsertion)
eventBases = nextEventBases;
else
eventBases = null; // ignore argument in any other case
if (isBeforeDeletion || isBeforeInsertion)
eventLength = nextEventLength;
else
eventLength = -1;
}
public boolean isDeletion() {
@ -104,6 +119,20 @@ public class PileupElement implements Comparable<PileupElement> {
return getBaseDeletionQual(offset);
}
/**
* Returns length of the event (number of inserted or deleted bases
*/
public int getEventLength() {
return eventLength;
}
/**
* Returns actual sequence of inserted bases, or a null if the event is a deletion or if there is no event in the associated read.
*/
public String getEventBases() {
return eventBases;
}
public int getMappingQual() {
return read.getMappingQuality();
}

10
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
View File

@ -71,7 +71,13 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
}
@Override
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
return new PileupElement(read, offset, isDeletion, isBeforeDeletion, 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, null,0);
}
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion,
boolean isNextToSoftClip,String nextEventBases, final int nextEventLength) {
return new PileupElement(read, offset, isDeletion, isBeforeDeletion, isBeforeInsertion, isNextToSoftClip, nextEventBases,nextEventLength);
}
}