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feat(#741): Pretty print#742

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andreasprlic wants to merge 36 commits intobiocommons:mainbiocommons/hgvs:mainfrom andreasprlic:pretty_printandreasprlic/hgvs:pretty_printCopy head branch name to clipboard

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Commits on May 13, 2024

• feat(pretty print): adding some experimental code for pretty printing hgvs variants.

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• feat(pretty print): making sure we don't bloat the test cache.

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• feat(pretty print): making type py3.8 compatible

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Commits on May 28, 2024

• feat(pretty print): breaking up creation of each line in display into subclasses

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Commits on May 29, 2024

• feat(pretty print): breaking up creation of each line in display into subclasses

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Commits on Jun 1, 2024

• feat(pretty print): feat(pretty print): improvements for RNA coding transcripts, new option to show reverse-chrom strand sequence.

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Commits on Jun 3, 2024

• feat(repeat-detection): using fully justified representation.

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• feat(repeat-detection): using fully justified representation.

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• formatting

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Commits on Jun 6, 2024

• feat(prot-pos): now showing the protein (amino acid) positions more clearly

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Commits on Jun 7, 2024

• feat(repeat-detection): now with better detection of repetitive units that are larger than 1 bp.

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• feat(repeat-detection): hooking repeat detection improvements in pretty print.

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Commits on Jun 9, 2024

• Merge branch 'main' into pretty_print

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Commits on Jun 30, 2024

• feat(pretty_print): now showing hgvs_p, making code more accessible for consumer

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• Merge branch 'main' of github.com:biocommons/hgvs into pretty_print

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• feat(ci): trying to get pytest to work again

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Commits on Jul 1, 2024

• feat(cleanup): removing cache from test_repeats. They are creating too big of a cache.

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Commits on Aug 13, 2024

• cleanup

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Commits on Sep 2, 2024

• biocommons#741 small refactoring to update directory structure, based on PR comments

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• Merge branch 'main' into pretty_print

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• biocommons#741 small refactoring to update directory structure, based on PR comments, also disabling slow running unit test

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Commits on Sep 6, 2024

• biocommons#741 excluding data intensive tests from CI. They would create too much caching burden.

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• trying to fix CI

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Commits on Sep 7, 2024

• feat(repeats): found an issue with count_pattern_occurences, fixed and with more unit tests.

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Commits on Sep 16, 2024

• feat(repeats): adding examples from HGVS repeats recommendations page. Improved repeat analyzer, that now supports 5' and 3' shuffling.

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Commits on Sep 17, 2024

• 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.

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Commits on Sep 19, 2024

• feat(repeats): moving max repeat config to global config. Also a small improvement at the loss of repeat check.

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• skipfeat(repeats): skipping more tests that are too data heavy.

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• feat(repeats): improvements in repeat check.

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Commits on Oct 3, 2024

• feat(reverse-strand): Now showing reverse strand transcript in 5'-3' orientation relative to the transcript by default (can be configured).

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• feat(is_rna): moving the check if a transcript is RNA only to datacompiler

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• fix

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Commits on Nov 16, 2024

• fixing off-by one error at transcript start, problematic intergenic variants, and only one assembly mapper on pretty print.

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Commits on Dec 24, 2024

• WIP

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Commits on Jan 20, 2025

• Merge branch 'main' into pretty_print

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• Merge branch 'main' into pretty_print

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