Breaking changes
- Command line arguments and options now use `key=value` syntax consistently (where applicable):
- auxiliary set option `--aux / -a` previously used whitespace to separate `key` and `value` but now uses `=` instead:
sh
vembrane filter --aux known_genes=known_genes.txt "ID in AUX['known_genes']" input.vcf
- The same holds for `--overwrite-number-info` and `--overwrite-number-format` options:
sh
vembrane filter --overwrite-number-format DP=1 "FORMAT['DP']['Sample'] == 0" input.vcf
- This also holds for the new `tag` subcommand (see below)
- The deprecated `--overwrite-number` option was removed (140)
Features
- Add `tag` subcommand (126):
The tag subcommand allows specifying multiple `--tag name=expression` arguments.
If a record *passes* an expression, the corresponding tag is added to its `FILTER` field.
To instead tag records which *fail* an expression, either invert the expressions or use the `--tag-mode fail` option.
Example:
sh
vembrane tag --tag quality_at_least_30="QUAL >= 30" input.vcf
- Introduce `get(item, default=NA)` methods for `INFO`, `ANN` and `FORMAT[field]` (139)
This is a convenience function for handling missing values (in existing fields), which will be replaced by the provided default value (which itself defaults to `NA`)
Example:
sh
vembrane filter "ANN.get('Impact', 'HIGH')"
Note that this will still `KeyError` when no such field has been defined in the header (e.g. `"ANN.get('nonexistent_key')"`)
- Add '.raw' getter property to custom types to get original annotation string (137)
Because `vembrane` has custom types for certain annotations, their string representation may be different from the string they were parsed from. These types now have a `.raw` property to access the original string, e.g. `ANN["EXON"].raw`
- Attribute access on `NA` values results in `NA` (136)
Example:
sh
vembrane table "ANN['EXON'].range.start" input.vcf
will no longer cause an `AttributeError` when the `ANN['EXON']` field is empty. This is because `NA.arbitrary_attribute` is now equivalent to `NA`.
- Support `--aux` for vembrane table. (142)
Previously, the `table` subcommand did not support auxiliary files -- now it does!
- Add support for new-ish gnomADe_* and gnomADg_* entries from VEP (134)
There have been some upstream changes with respect to gnomAD naming conventions, which are now split into exome (e) and genome (g) populations. This simply adds support for the new names.
Fixes
- Fix regex for checking tag names, add more help to tag option (141)
- Add testcase for `table --aux` (144)
- `PosRange` specific fixes (138)
Housekeeping
- Update dependencies (145)
- Address some mypy errors and hints (143)