non ACGT Bug fix kinda

[migbro]

Going on the premise that GATK's outputs are wildly popular and that in their format, * is a valid alt possibility, even if in practice you would not use it:

• allow * as acceptable value
• However, other characters would still cause the bug to reappear, like if there was an N
  Separately, I :revert vec as change in main as it causes compile fail. Also a small update to git ignore to avoid test files

Fixes #36

[migbro]

Been talking with @dmiller15 about this and don't really like my solution. It'd be preferred to simply skip annotating *alleles - like still output the line as-is. Unfortunately, not really sure how to do that or if it'd require major refactoring. It's something I think a lot of people who use GATK for germline trio calls will encounter

[brentp]

I don't think this will work anyway, the encoding uses 2 bits per letter so only ACTG can be encoded.

[migbro]

Yeah, that's fair. I'll dump this PR, pull your other bug fix and ruminate some more. We've been working to incorporate this tool as an annotation replacement for bcftools to annotate thousands of germline vcfs with a subset of gnomAD 3.1.1 fields, hence my eagerness to tighten up a couple things. It's speed will save a us a good chunk of time and money collectively

[brentp]

We've been working to incorporate this tool as an annotation replacement for bcftools to annotate thousands of germline vcfs with a subset of gnomAD 3.1.1 fields, hence my eagerness to tighten up a couple things. It's speed will save a us a good chunk of time and money collectively

Let's figure out how to get it in a state where you can use it.
Can you let me know if it's ok with you to discard variants with "*" in the archive set and just skip them (write out without annotation) in the query set?

[migbro]

The short answer is probably yes. This is predicated on, if I understand correctly, encoder is used to process input vcfs in both encode and anno modes. So, I'd think since it's not designed to handle ACGT, it's probably ok to skip encoding non ACGT in the zips generated, as long as if a non ACGT character in the vcf being annotated still shows up as-is with no annotation in the annotated result from anno. Does that make sense?

[migbro]

Alternatively, perhaps as a future feature, you could consider expanding to the complete IUPAC notation while keeping the same behavior to skip encoding non-conforming characters to cover nearly all possible use cases. That's probably make the bit encoding more complex and the resulting binaries larger. Not sure how speed would be affected