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
(These commits should have been made to 1.5 branch)
…NCBI failures (2020-03-28, all day)
…alignment methods (#597)
…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
* use same data sources for learning and testing in Makefile * tests appear to work with cached results * udpate misc/docker-compose.yml for testing setup * update tests using misc/docker-compose.yml stack * add target to build test cache iteratively * fill in additional test data * fix UTA_DB_URL * attempt to make gitguardian ignore secret * run on push or pull_request, but not both * remove push/pr dedupe for now; try a different way to have gitguardian ignore secret * revert unnecessary changes back to main * revert unnecessary changes back to main * update README with instuctions for loading the test caches --------- Co-authored-by: Reece Hart <[email protected]>
* feat(pretty print): adding some experimental code for pretty printing hgvs variants. * feat(pretty print): making sure we don't bloat the test cache. * feat(pretty print): making type py3.8 compatible * feat(pretty print): breaking up creation of each line in display into subclasses * feat(pretty print): breaking up creation of each line in display into subclasses * feat(pretty print): feat(pretty print): improvements for RNA coding transcripts, new option to show reverse-chrom strand sequence. * feat(repeat-detection): using fully justified representation. * feat(repeat-detection): using fully justified representation. * formatting * feat(prot-pos): now showing the protein (amino acid) positions more clearly * feat(repeat-detection): now with better detection of repetitive units that are larger than 1 bp. * feat(repeat-detection): hooking repeat detection improvements in pretty print. * feat(pretty_print): now showing hgvs_p, making code more accessible for consumer * feat(ci): trying to get pytest to work again * feat(cleanup): removing cache from test_repeats. They are creating too big of a cache. * cleanup * #741 small refactoring to update directory structure, based on PR comments * #741 small refactoring to update directory structure, based on PR comments, also disabling slow running unit test * #741 excluding data intensive tests from CI. They would create too much caching burden. * trying to fix CI * feat(repeats): found an issue with count_pattern_occurences, fixed and with more unit tests. * feat(repeats): adding examples from HGVS repeats recommendations page. Improved repeat analyzer, that now supports 5' and 3' shuffling. * feat(repeats): adding an example of a large variant to make sure we don't run repeat analysis where it does not make sense. Starting to add support for non-splign alignments. * feat(repeats): moving max repeat config to global config. Also a small improvement at the loss of repeat check. * skipfeat(repeats): skipping more tests that are too data heavy. * feat(repeats): improvements in repeat check. * feat(reverse-strand): Now showing reverse strand transcript in 5'-3' orientation relative to the transcript by default (can be configured). * feat(is_rna): moving the check if a transcript is RNA only to datacompiler * fix * fixing off-by one error at transcript start, problematic intergenic variants, and only one assembly mapper on pretty print. * WIP * addressing comments on PR * bringing in sync with main * removing dependency on parameterized again.
Co-authored-by: Reece Hart <[email protected]>
* Fix exception in g_to_c mapping * Use fixtures from conftest.py
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