Filtering lower-case letters from pileup?

[stschiff]

v1.5.2 introduced a feature whereby lower-case letters in the pileup-input are automatically parsed as capital-letters and thereby fully considered when calling the alleles. This may be appropriate in many cases, but sometimes lower-case letters signify lower-quality or masked reads, so there may be a point to not parse these.

We might want an option to ignore lower-letter reads.