/** * 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); }