Pyvariant

Bugfixes:

- Fix the 5' and 3' bases flanking insertions being added twice when window is used in the sequence method
- Fix negative positions being passed to the sequence fetching method, causing the wrong reference sequence to be returned


**Full Changelog**: https://github.com/mattdoug604/pyvariant/compare/v2.2.3...v2.2.4

Bugfixes
* fix dna variants on the - strand having the reverse-complement altseq

**Full Changelog**: https://github.com/mattdoug604/pyvariant/compare/v2.2.2...v2.2.3

Changes:
- assume protein duplications are due to a nucleotide insertion when mapping by default

Bugfixes:
- fix sequence fetch failing when window extends past feature start
- reduce the memory footprint of reverse_translating long proteins
- speed up mapping protein duplications
- fix parsing for frameshift variants in hgvs notation
- fix sequence mutation when site is at sequence end

**Full Changelog**: https://github.com/mattdoug604/pyvariant/compare/v2.2.1...v2.2.2

Bugfixes:
* fix insertions and frameshifts parsed from strings being interpreted as delins

Minor:
* add unit test for expanding empty strings
* ignore lock files in repo

Features:
* support parsing variants in the intron of a promoter region
* add ExonSmallVariant class

Changes:
* rename 'positions' module to 'variants'
* allow versions of gtfparse<=2.0.1

Bugfixes:
* remove lru_cache decorators from alias functions so that alias attribute can be overridden by user

Features:
* add mapping methods to variant objects
* add parameterize tests and test data
* all functions to be passed as alias input

Bugfixes:
* rename env 'VARIANT_MAP_CACHE' to 'PYVARIANT_CACHE'
* fix test fasta missing sequence; update tests