VariantEffect / mavedbconvert / 29

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test coverage 100% (#13)

* ref allele of "?" shouldn't validate

* use abstract base classes

* fix # pragma statements

* test additional exceptions

* remove deleted test cases

* disable logging output for tests

* couldn't figure out how to raise this in tests

* add permission error mocks

* black formatting

* use base class temp directory

* fix up imports

* use fqfa sequence validation

* parsers don't need to know variant format

* check for support of noncoding datasets

* remove unused import

* always drop na inplace

* remove self.bin from tests

* black formatting

* move tests out of module

* use default temp location

* drop removed modules

* unused import

* wrote generic hgvs uniqueness check

* remove tests for zero-based protein variants

These variants were not being generated by any module code, since utilities.ProteinSubstitutionEvent generates one-based positions.

* add coverage config file

* update tests for hgvs uniqueness

* fix typo

* remove unnecessary check for special variants

* unknown wild-type amino acid shouldn't validate

* more test cleanup

* linting and dead code removal

* test using convert() method

* full test coverage for enrich and empiric

* add tests and fix edge case with special variants

* split huge parsing test into a new file

* full test coverage but enrich2 tsv needs work

526 of 526 branches covered (100.0%)

Branch coverage included in aggregate %.

71 of 71 new or added lines in 7 files covered. (100.0%)

1092 of 1092 relevant lines covered (100.0%)

4.0 hits per line