What is the non-deprecated replacement for acceptableAlleleBases?

[danking]

Description of the issue:

Hail is trying to update to htsjdk 3.x.x. We currently use Allele.acceptableAlleleBases. This fails our build system because its deprecated. Is there a replacement for this method or is it being intentionally removed from the public API?

Your environment:

htsjdk==3.0.1

Steps to reproduce

Compile something that uses htsjdk.variant.variantcontext.Allele.acceptableAlleleBases with warnings are errors (-Xfatal-warnings).

[lbergelson]

@danking This is a good question. I think the reasoning for deprecating that method has been lost in the extremely long time the PR sat and perhaps should not have been deprecated. It seems like it got caught in the drive to remove the awkwardly named "wouldBe" methods. I don't see any reasonable replacement at the moment other than trying to create an Allele and catching the inevitable exception which is not a good workflow. I'm going to de-deprecate it for 3.0.2.

[danking]

Thanks @lbergelson !

[lbergelson]

@danking 3.0.2 is on it's way to maven central and should be visible with in the next hour or so.

[danking]

Thank you!