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Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper 

* New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches.
    * Added functionality to clipping op to revert all soft clip bases in a read into matches
    * Added revertSoftClipBases function to the ReadClipper for public use
    * Wrote systematic unit tests
This commit is contained in:
Mauricio Carneiro 2011-12-19 14:56:19 -05:00
parent 24585062f8
commit 78d9bf7196
4 changed files with 74 additions and 7 deletions
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38
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
View File

@ -104,6 +104,10 @@ public class ClippingOp {
break;
case REVERT_SOFTCLIPPED_BASES:
read = revertSoftClippedBases(read);
break;
default:
throw new IllegalStateException("Unexpected Clipping operator type " + algorithm);
}
@ -111,6 +115,38 @@ public class ClippingOp {
return read;
}
private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
GATKSAMRecord unclipped;
// shallow copy of the read bases and quals should be fine here because they are immutable in the original read
try {
unclipped = (GATKSAMRecord) read.clone();
} catch (CloneNotSupportedException e) {
throw new ReviewedStingException("Where did the clone go?");
}
Cigar unclippedCigar = new Cigar();
int matchesCount = 0;
for (CigarElement element : read.getCigar().getCigarElements()) {
if (element.getOperator() == CigarOperator.SOFT_CLIP || element.getOperator() == CigarOperator.MATCH_OR_MISMATCH)
matchesCount += element.getLength();
else if (matchesCount > 0) {
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
matchesCount = 0;
unclippedCigar.add(element);
}
else
unclippedCigar.add(element);
}
if (matchesCount > 0)
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
unclipped.setCigar(unclippedCigar);
unclipped.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), unclippedCigar));
return unclipped;
}
/**
* Given a cigar string, get the number of bases hard or soft clipped at the start
*/
@ -472,7 +508,7 @@ public class ClippingOp {
for (CigarElement cigarElement : oldCigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
oldShift += cigarElement.getLength();
else if (readHasStarted)
break;
}

7
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
View File

@ -29,5 +29,10 @@ public enum ClippingRepresentation {
* lossy) operation. Note that this can only be applied to cases where the clipped
* bases occur at the start or end of a read.
*/
HARDCLIP_BASES
HARDCLIP_BASES,
/**
* Turn all soft-clipped bases into matches
*/
REVERT_SOFTCLIPPED_BASES,
}

5
public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
View File

@ -213,4 +213,9 @@ public class ReadClipper {
}
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public GATKSAMRecord revertSoftClippedBases() {
this.addOp(new ClippingOp(0, 0)); // UNSOFTCLIP_BASES doesn't need coordinates
return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
}
}

31
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
View File

@ -279,9 +279,9 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
int expectedLength = read.getReadLength() - leadingCigarElementLength(read.getCigar(), CigarOperator.INSERTION);
if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
expectedLength -= leadingCigarElementLength(ReadClipperTestUtils.invertCigar(read.getCigar()), CigarOperator.INSERTION);
if (! clippedRead.isEmpty()) {
Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString())); // check that everything else is still there
@ -293,6 +293,27 @@ public class ReadClipperUnitTest extends BaseTest {
}
}
@Test(enabled = true)
public void testRevertSoftClippedBases()
{
for (Cigar cigar: cigarList) {
final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
final int tailSoftClips = leadingCigarElementLength(ReadClipperTestUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
final GATKSAMRecord unclipped = (new ReadClipper(read)).revertSoftClippedBases();
if ( leadingSoftClips > 0 || tailSoftClips > 0) {
final int expectedStart = read.getAlignmentStart() - leadingSoftClips;
final int expectedEnd = read.getAlignmentEnd() + tailSoftClips;
Assert.assertEquals(unclipped.getAlignmentStart(), expectedStart);
Assert.assertEquals(unclipped.getAlignmentEnd(), expectedEnd);
}
else
Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
}
}
private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {
@ -304,12 +325,12 @@ public class ReadClipperUnitTest extends BaseTest {
}
private boolean startsWithInsertion(Cigar cigar) {
return leadingInsertionLength(cigar) > 0;
return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
}
private int leadingInsertionLength(Cigar cigar) {
private int leadingCigarElementLength(Cigar cigar, CigarOperator operator) {
for (CigarElement cigarElement : cigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.INSERTION)
if (cigarElement.getOperator() == operator)
return cigarElement.getLength();
if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
break;