update VRS annotation batch script for v4 exomes

[KoalaQin]

There are a few changes implemented to make the run:

1. add function for the output path of VRS in v4 exomes;
2. Delete other v3 input and output paths in the dictionary;
3. put retry in init_job_with_gcloud to avoid Hail Batch transient errors, suggested by Dan King;
4. add bgzip in --run-vrs step so import_vcf could be run faster;
   5. move import_vcf to --annotate-original step because this is faster to run in Query-on-Spark (QoS);
   6. remove checkpoint since we know where the final folder of the VRS annotations
5. remove delete_temps because files got removed even if the jobs weren't all successful;
6. change exclude duplicate so it applies to only one input file;
7. use gnomad-tmp-4day in working-bucket, so the intermediate files can be automatically deleted);
   10. Clarify in the docstring that the script has to be run once on QoB, once on QoS.

update 2023-08-16:

1. add test argument to test on 200 partitions;
2. put annotate-original back to original design, now with hailctl batch submit we can run both run-vrs and annotate-original in one go

[KoalaQin]

@klaricch I changed the code, to add a test argument to test 200 partitions of an input, and put annotate-original back to what it was, and now with hailctl batch submit we can run both run-vrs and annotate-original in one go.

[KoalaQin]

@klaricch annotations.py is identical to main now, I couldn't merge main into this branch because it's been there too long.

[KoalaQin]

@klaricch I made changes to get rid of vrs-io-finals, but you can't test with hailctl batch submit yet (because the docker image needs to be updated with the annotations.py). I ran a test with this and it worked:

python3 /Users/heqin/PycharmProjects/gnomad_qc/gnomad_qc/v4/annotations/vrs_annotation_batch.py \
--billing-project gnomad-annot \
--working-bucket gnomad-tmp-4day \
--image us-central1-docker.pkg.dev/broad-mpg-gnomad/images/vrs084 \
--version test_v4.0_exomes \
--prefix v4 \
--header-path gs://gnomad/v4.0/annotations/exomes/vrs-header-fix.txt \
--run-vrs \
--annotate-original \
--overwrite \
--backend-mode batch \
--test

[klaricch]

lgtm