ClipReads tool - only at end of read?

I would like to use the ClipReads tool to soft clip reads (in a bam file) that contain an exact match to a set of sequences (primer seqs). ClipReads should be able to do this, but the problem is with overlapping amplicon regions. with overlapping regions, the primer seq may legitimately appear in the middle of read (as actual sample sequence) and the ClipRead tool will mask it.

Is there a way to instruct ClipReads to only clip reads when a sequence match is found at the END OF READS?

thanks.