Add param --quality_type

[d4straub]

The parameter --quality_type is added that allows specifying the quality encoding instead of relying on automatic inference thereof.
Unfortunately dada() seems not to be able to use quality type information, therefore the data needs to be read by derepFastq() first. That is a disadvantage for computational resources, so its only used when necessary, i.e. when not --quality_type "Auto".

Closes #773

This is still a draft PR, because (1) I didnt test it on actual data and (2) test data would be great.

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