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I have a question concerning the ClipReads function and the different functionalities it's offering. The --clipRepresentation option and the different possibilites it offers doesn't seems to do what it's supposed to... As a matter of fact, I tried the REVERT_SOFTCLIPPED_BASES and HARDCLIP_BASES options and those seem unefficient while giving in input bam files coming from bwa.
HARDCLIP_BASES seems to do what REVERT_SOFTCLIPPED_BASES is supposed to do. I end up using that as it's doing what I want. However, do you think it could be possible to add an option to change the base qualities of those bases that were reverted as we do not necessarily want to include them by using different BQ thresholds?
Thanks a lot!