/**
* Checks if a read contains adaptor sequences. If it does, hard clips them out.
*
* <p>Note: To see how a read is checked for adaptor sequence see ReadUtils.getAdaptorBoundary()
*
* @return a new read without adaptor sequence
*/
private GATKSAMRecord hardClipAdaptorSequence() {
final int adaptorBoundary = ReadUtils.getAdaptorBoundary(read);
if (adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY
|| !ReadUtils.isInsideRead(read, adaptorBoundary)) return read;
return read.getReadNegativeStrandFlag()
? hardClipByReferenceCoordinatesLeftTail(adaptorBoundary)
: hardClipByReferenceCoordinatesRightTail(adaptorBoundary);
}
