Flexible filtering of reads for pileupcaller genotyping.

[TCLamnidis]

Small quality of life change. Rather than hardcoding map and base quality filtering of 30 prior to pileupcaller genotyping, the two filters can now be custom set with --pileupcaller_min_map_quality and --pileupcaller_min_base_quality.

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
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• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
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