Vembrane

Changes

- Only allow one ALT allele per record, error if more than one is encountered tedil (73)
*This change affects expression syntax and VCF input requirements*:
- VCF files need to be split such that each record has only one ALT allele, this can be achieved with e.g. the following tools:
- [`bcftools norm -m-any […]`](http://samtools.github.io/bcftools/bcftools.html#norm)
- [`gatk LeftAlignAndTrimVariants […] --split-multi-allelics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037225872-LeftAlignAndTrimVariants)
- [`vcfmulti2oneallele […]`](http://lindenb.github.io/jvarkit/VcfMultiToOneAllele.html)
- This makes filter expressions way less verbose and easier to use; instead of `ALT[0] == "C" and INFO["gnomad_AF"][0] > 0.01` (where `0` is the index of the first ALT allele), use `ALT == "C" and INFO["gnomad_AF"] > 0.01`. (This does reduce expressiveness a bit since you cannot reason about, say, the sum of alternate allele frequencies anymore)
- (Also consider splitting your VCF files *before* annotating with snpeff/vep/etc.)
- Export NA to enable checks such as `INFO["DP"] is NA` tedil (74)
- bool(NA) = False christopher-schroeder (72)

Changes

- Remove header.info from globals mbargull (70)
- Use `NA` as default for INFO fields which appear in the header but not in the record mbargull (70)
- Allow more builtins christopher-schroeder (67) (68) mbargull (69)

Features

- move globals_whitelist to own module mbargull (69)

Changes

- Swap order of access for FORMAT from `sample → field` to `field → sample` tedil (65)
- Try evaluating the filter expression for the first record before writing the VCF header tedil (66)
- Swap expression and VCF input positional arguments, make input default to stdin tedil (62)

Features

- Parse info/annotation entries only on dict lookup mbargull (63).
Bug Fixes

- Replace hardcoded "ANN" in `statistics` with `ann_key` tedil (60)

Changes

- Check for annotation_key in the filter expression via walking the ast tedil (54)

Bug Fixes

- Replace usages of "ANN" with annotation-key specified on the CLI tedil (53)

Maintenance

- Fix github workflow for publishing to PyPI tedil (59)
- Use the maintenance label for github and packaging related work tedil (55)
- Add missing template for release draft GitHub workflow tedil (52)
- Manage version via pyproject.toml only tedil (51)
- Add release drafter GitHub workflow tedil (50)
- Github workflow for building the vembrane dists and publishing them to PyPI tedil (49)

* add support for VEP annotation fields
* unify access to VCF fields (all uppercase: FORMAT, QUAL, INFO, etc and ANN
* only evaluate expression once if no ANN annotation is used
* code refactoring
* better error disambiguation
* additional tests

Initial release of `vembrane`.