Pull updated hgvs into vvhgvs to bring vv in line with hgvs.py #7
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* added docker-compose file and updated README
* started CIGARMapper (incomplete)
* incorporated alignmentmapper into cigarmapper module for testing/comparison
* more cleanup of new cigarmapper and comparisons
* initial migration of alignmentmapper to cigarmapper; some tests still fail
* added mapper.strict_transcript_bounds option to config
* streamlined test_hgvs_alignmentmapper to facilitate comparison (in future commits)
* checkpoint of non-functional code; changing strategy
* alignmentmapper.py → alignmentmapper_new.py
* alignmentmapper_old.py → alignmentmapper.py
* tests pass again
* Factored CIGARMapper out of AlignmentMapper (take 2); tests pass!
* untangled AlignmentMapper's use of private data and methods
* moved CIGARMapper to separate module; tests pass
* removed alignmentmapper_new.py
* renamed mapping arg `base` to `end`
* moved parse_cigar to alignmentmapper
* added cigarmapper tests
* rename parse_cigar to _parse_cigar
* added strict_bounds flag to cigarmapper (default=True; not yet in alignmentmapper)
* added new strict_bounds flag to alignment mapper methods, with default from global_config
* added tests for issue 437 (and they pass!)
* removed unnecessary validation check
* rename legacy r_{start,end} to n_{start,end} for consistency elsewhere
* minor test rearrangement
* update cigarmapper test alignment docs for clarity about intent
* fixed recently introduced bug that considered last base of transcript as out-of-bounds
* fixed bug caused by test data missing from cache, inexplicably
* adding more missing data from cache
* fixed incorrect test of 3' terminus
* rename 437 tests
* removed alignmentmapper exception tests that no longer apply
* support negative n. coordinates
* reworked #437 tests to use fixtures to speed up tests
* verified and reenabled test for NR_003051.3:n.-19_-18insACT
* added g-to-n tests, but some fail and need to be addressed (marked `#BUG:`)
* use HGVS_LOGGING_LEVEL env var to customize logging level
* left normalize transcript variant on genomic sequence when - strand and out-of-bounds
* updated config info to include `strict_bounds`
… infer ref from genomic sequence
…t normalize an oob variant
…n strict_bounds=True
#178 - use abc for Edit class to ensure method definition
* Update default UTA version to 20210129b * Use `literalinclude` to present default configs in docs rather than copy/pasting * Clean up tests to be less brittle re: data updates in UTA --------- Co-authored-by: Andreas Prlic <[email protected]> Co-authored-by: Kori Kuzma <[email protected]>
…ccessions #744 - babelfish vcf conversion accept contig accessions as chrom names
Co-authored-by: Kori Kuzma <[email protected]>
Fix for issue 704 - pass on prevalidation_level
…etained fix: projection issue for stop retained insertion (#707)
* also updates checkout + setup-python action versions in test
#755) * set record_mode to fix failing tests * ci uses 'none' * default uses 'new_episodes' (can overide via VCR_RECORD_MODE env var) * re-ran cassettes to update with the correct config
Update authors for 2024 (last updated 4 years ago)
Remove python2 legacy
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