Nils Homer
Nils Homer
`python setup.py test` or `python setup.py install` gives the error message below. I wanted to test my PR https://github.com/brentp/cyvcf2/pull/98 locally. ``` 20 warnings generated. gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g...
If the `PS` format field has type `Integer` but the _values_ are strings, then `cyvcf2` will skip the variant but not throw an exception. I would have expected, by default,...
I'd like to build a _new_ `Variant` without and input VCF, and then write it to a file. I was hoping to see such an example in the test classes,...
I want to have a single rule retried but all other rules fail after one retry. This is currently not possible for `--restart-times` I believe. For the single rule I...
I would like to be able to create type aliases, namely something like this: ``` ... type PathToFastq = File type PathToFasta = File ... task bwa { input {...
How to apply a protein change to a given amino acid sequence to produce a mutant amino acid sequence
I was thinking it would be in one of the mapping or projection classes, but I couldn't find one. I don't want to have to rely on transcript sequence database...
Related to #581. If we have `DUMMY:c.2_4dupATC`, then I was expecting the [`Dup` class](https://github.com/biocommons/hgvs/blob/9386562cd7c61b7f6ec6c556adcd99e3dfffaa62/hgvs/edit.py#L399) to have both a `ref` AND `alt` defined. Currently, it only has `ref` defined. The HGVS...
This is so that I can have assembled molecules first, whereas in some assembly reports chrM (an assembled molecule) is listed at the end of the report.