Update notebooks, alignment, and mapping code

[jarbesfeld]

• Update analysis notebooks to reference the summary statistics in the updated preprint
• Update alignment code to ensure correct BLAT parameters are being used and that the correct strand orientation is selected for protein coding DNA target sequences
• Update vrs_map to skip protein mapping when only genomic variants should be mapped

[jsstevenson]

The tests still assume that the extra objects get created -- I think behavior is correct so we should update the expected values so that they pass in CI. Can work through that with you if it gives you trouble.

[jsstevenson]

👍 looks good, a couple small changes

[jsstevenson]

blank line between the first sentence in the docstring and the first :param: line

[jsstevenson]

looks like tests are failing now fyi