/**
* Calculates the reference coordinate for the end of the read taking into account soft clips but
* not hard clips.
*
* <p>Note: getUnclippedEnd() adds soft and hard clips, this function only adds soft clips.
*
* @return the unclipped end of the read taking soft clips (but not hard clips) into account
*/
public int getSoftEnd() {
if (softEnd == UNINITIALIZED) {
boolean foundAlignedBase = false;
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 (op
== CigarOperator
.SOFT_CLIP) // assumes the soft clip that we found is at the end of the aligned read
softEnd += cig.getLength();
else if (op != CigarOperator.HARD_CLIP) {
foundAlignedBase = true;
break;
}
}
if (!foundAlignedBase) { // for example 64H14S, the soft end is actually the same as the
// alignment end
softEnd = getAlignmentEnd();
}
}
return softEnd;
}
