Add a mergeWithRemapping() method in ReferenceConfidenceVariantContextMerger to perform allele remapping prior to genotyping

[droazen]

This is intended to tide the GVS team over until #8317 is fixed.

[droazen]

@mcovarr Could you please try the new ReferenceConfidenceVariantContextMerger.mergeWithRemapping() method out in the GVS branch, and report whether your tests pass? Should be a drop-in replacement for ReferenceConfidenceVariantContextMerger.merge().

Once #8317 is fixed, we'll make this behavior the default and ask you to switch back to merge(), as discussed recently.

[droazen]

@ldgauthier At some point I'd like to discuss both this PR and #8317 with you

[gatk-bot]

Github actions tests reported job failures from actions build 4962783051
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	4962783051.10	logs
cloud	17.0.6+10	4962783051.10	logs
cloud	17.0.6+10	4962783051.10	logs
cloud	17.0.6+10	4962783051.10	logs

[droazen]

(Note that the failure in the cloud tests is expected due to an ongoing GCS bucket region migration -- it should clear up next week)

[mcovarr]

LGTM, thank you! Confirmed that mergeWithRemapping works on the GVS / master branch here.

[droazen]

Merging this one despite the ongoing failure in the cloud tests, which is understood and known to be unrelated.