I am getting an error when trying to soft clip bases with ClipReads --clipSequence that the sequences I am trying to clip are not at the end of a read. I can see this is mentioned in the documentation as being the correct behaviour. However, I would would still like to get a sofclipped BAM as output
Would it be possible to add a --validation_strictness LENIENT option which would allow this error to be overridden? i.e. ignore any matched sequences not at the ends of a read but still clip matches at the beginning of reads?