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Hard clipping soft clipped reads to fix misalignments. 

Pre-softclipped reads (with high qual) are a complicated event to deal with in the Reduced Reads environment. I chose to hard clip them out for now and added a todo item to bring them back on in the future, perhaps as a variant region.
This commit is contained in:
Mauricio Carneiro 2011-09-21 17:12:01 -04:00
parent b36d396c16
commit 70335b2b0a
1 changed files with 35 additions and 0 deletions
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35
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.clipreads;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
@ -8,6 +9,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
@ -128,6 +130,39 @@ public class ReadClipper {
return this.clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public SAMRecord hardClipSoftClippedBases () {
int readIndex = 0;
int cutLeft = -1; // first position to hard clip (inclusive)
int cutRight = -1; // first position to hard clip (inclusive)
boolean rightTail = false; // trigger to stop clipping the left tail and start cutting the right tail
for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.SOFT_CLIP) {
if (rightTail) {
cutRight = readIndex;
}
else {
cutLeft = readIndex + cigarElement.getLength() - 1;
}
}
else
rightTail = true;
if (cigarElement.getOperator().consumesReadBases())
readIndex += cigarElement.getLength();
}
// It is extremely important that we cut the end first otherwise the read coordinates change.
if (cutRight >= 0)
this.addOp(new ClippingOp(cutRight, read.getReadLength() - 1));
if (cutLeft >= 0)
this.addOp(new ClippingOp(0, cutLeft));
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
/**
* Return a new read corresponding to this.read that's been clipped according to ops, if any are present.
*