Update TODO.md

Author: jsstevenson

TODO.md

@@ -5,8 +5,9 @@ General:
 * Docker-ification. (there should be existing images for SeqRepo and UTA, not sure how up-to-date they are).
 * Add extra stuff that appears in mapping JSON objects (``vrs_ref_allele_seq``).
 * Currently using VRS 2.0a-based libraries. For lifting back to VRS 1.3, some basic post-processing should be fine (annoying but shouldn't be too trivial)
-* Without access to a production DynamoDB instance, Gene Normalizer will be quickest and easiest to set up via a PostgreSQL data backend. That, however, requires an extra dependency group (noted in README). We might want to make a `pg` dependency group here or just include it in core dependencies.
+* Without access to a production DynamoDB instance, Gene Normalizer will be quickest and easiest to set up via a PostgreSQL data backend (https://gene-normalizer.readthedocs.io/en/latest/install.html#quick-installation). That, however, requires an extra dependency group (noted in README). We might want to make a `pg` dependency group here or just include it in core dependencies. 
 * On that note, I've only done minimal testing of how possible it would be to drop the gene normalizer dependency entirely, but it'd be nice to get there.
+* Pickle files for most of the checkpoint objects are available here: https://mavedb-mapping.s3.us-east-2.amazonaws.com/dcd_mapping_pickles.zip
 
 Alignment:
 * Pretty sure this is mostly done.
@@ -15,6 +16,7 @@ Alignment:
 Transcript selection:
 * IndexError in calculating offset on lots of new (2023) scoresets.
 * Tests will need some extensive mocking (or cassettes?) for reliance on UTA and other external dependencies
+* Some discrepancies between original mappings and the output of this pipeline with respect to transcripts being tagged as `MANE Select` vs `MANE Plus Clinical`, as mentioned on the call. We haven't exhaustively determined scope of this but Jeremy Arbesfeld can help if there are further questions about this.
 
 VRS mapping:
 * In general, this stuff is still pretty rough. Not passing informal tests, and needs formal tests.