Extend max depth threshold

[standage]

By default, pysam limits pileups to 8000 reads max depth. This update overrides that default with 1000000, and exposes the parameter to the CLI.

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• [x] Changes are clearly described above
• [x] Any relevant issue threads are referenced in the description
• [ ] Any new features are tested (see docs/DEVEL.md for details)
• [x] Substantial changes are documented in CHANGELOG.md (see https://keepachangelog.com/en/1.0.0/)