Processing soft-clipped reads

[PeteHaitch]

methtuple has in principle support for soft-clipped reads as of v1.3. However, as Bismark does not allow soft-clipped reads this hasn't been tested. I will test this more thoroughly once I am update methtuple to use an aligner that allows soft-clips. See also the now-closed #45

[PeteHaitch]

As of v0.16.1, Bismark still uses Bowtie2 in end-to-end mode and so does not produce any soft-clipped reads. Therefore handling soft-clipped is still a non-issue although it is in principle supported by methtuple.