clipping recommendations

[bwlang]

In issue #47 , @abdeljalil-senhaji asks about whether it's a good idea to clip reads.

I do think it's good to trim adapter sequences, especially in 3-base context like EM-seq, since reads with adapter still present will align and produce artifacts. I also think it's good to eliminate poly-G regions of reads (as we do automatically) since they also can align to a few human genomic loci that are poly-C.

Unless there is a problem with the run, I see no benefit to trimming sequences either to account for end-repair methylation erasure or instrument-estimated lower quality. We do "trim" reads by default during methylation calling to account for end-repair effects, but these bases are useful for alignment purposes.