Vs 1416 modify ingest to correctly handle ploidy differences in dragen 3 7 8 samples

[koncheto-broad]

Three major changes here.

1. Added in logic to create the ploidy table during ingest (with necessary supporting class) and use it during extract automatically as part of the default joint workflow. Also removed a column that we won't need when creating it automatically.
2. Rearranged the PAR checking logic to consolidate it in its own class (PloidyUtils.java).

Successful run against tiny sample set "PLOIDY_TEST" in echo callset project:

https://app.terra.bio/#workspaces/allofus-drc-wgs-dev/GVS%20AoU%20WGS%20Echo%20Callset%20v2/job_history/a93aa2ef-9cef-451d-8cf8-b31f1c6a8407

You'll need your aou credentials to see the results.

Successful integration run on XY:
https://app.terra.bio/#workspaces/gvs-dev/GVS%20Integration/job_history/6a9a5fdf-ffaa-4dcb-af73-56a4b25e69a4

This run shows all of the OTHER integration tests running successfully except BGE, due to the test data needing an updates for BGE X and Y:
https://app.terra.bio/#workspaces/gvs-dev/GVS%20Integration/job_history/21664810-7516-49f2-a60c-51b2e05faf06

The only difference between those two tests running was an update to the expected values for integration tests

[gatk-bot]

Github actions tests reported job failures from actions build 11256533054
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11256533054.11	logs
integration	17.0.6+10	11256533054.0	logs

[gbggrant]

Looks good to me. Thumbs up, conditional on:

1. Miguel's comments are addressed.
2. Passing integration test (ideally on ALL chromosomes).

[gatk-bot]

Github actions tests reported job failures from actions build 11502878660
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11502878660.11	logs
integration	17.0.6+10	11502878660.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 11506462963
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11506462963.11	logs
integration	17.0.6+10	11506462963.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 11506500757
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11506500757.11	logs
integration	17.0.6+10	11506500757.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 11519677920
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11519677920.11	logs
integration	17.0.6+10	11519677920.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 11580320242
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11580320242.11	logs
integration	17.0.6+10	11580320242.0	logs

[gbggrant]

CreateVariantIngestFilesIntegrationTest test is failing now.

[gatk-bot]

Github actions tests reported job failures from actions build 11619790404
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	11619790404.11	logs
integration	17.0.6+10	11619790404.0	logs

[mcovarr]

minor nit only 👍

[mcovarr]

TOL should this 0.05 be a named constant? Or configurable?

[mcovarr]

actually it looks like there are legit failing tests

[koncheto-broad]

actually it looks like there are legit failing tests

Yup, it looks like a hunk of the integration tests are operating in TSV mode (which we don't officially support any longer... but I suppose they can stay). So in order to make those pass, I had to put some things behind an explicit check for BQ being set as the output type