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Better implementation for getSoftEnd() in GATKSAMRecord

This commit is contained in:
Eric Banks 2012-10-18 09:01:51 -04:00
parent 20ffbcc86e
commit 54f698422c
1 changed files with 12 additions and 15 deletions
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27
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
@ -406,24 +407,20 @@ public class GATKSAMRecord extends BAMRecord {
* @return the unclipped end of the read taking soft clips (but not hard clips) into account
*/
public int getSoftEnd() {
if (softEnd < 0) {
int stop = this.getUnclippedStart();
if ( softEnd < 0 ) {
softEnd = getAlignmentEnd();
final List<CigarElement> cigs = getCigar().getCigarElements();
for (int i=cigs.size() - 1; i>=0; --i) {
final CigarElement cig = cigs.get(i);
final CigarOperator op = cig.getOperator();
if (ReadUtils.readIsEntirelyInsertion(this))
return stop;
int shift = 0;
CigarOperator lastOperator = null;
for (CigarElement cigarElement : this.getCigar().getCigarElements()) {
stop += shift;
lastOperator = cigarElement.getOperator();
if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP || cigarElement.getOperator() == CigarOperator.HARD_CLIP)
shift = cigarElement.getLength();
else
shift = 0;
if (op == CigarOperator.SOFT_CLIP)
softEnd += cig.getLength();
else if (op != CigarOperator.HARD_CLIP)
break;
}
softEnd = (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
}
return softEnd;
}