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feat(#741): Pretty print #742

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feat(#741): Pretty print #742

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Commits on May 13, 2024

  1. feat(pretty print): adding some experimental code for pretty printing… 

    … hgvs variants.
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    andreasprlic committed May 13, 2024
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  2. feat(pretty print): making sure we don't bloat the test cache.

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    andreasprlic committed May 13, 2024
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  3. feat(pretty print): making type py3.8 compatible

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    andreasprlic committed May 13, 2024
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Commits on May 28, 2024

  1. feat(pretty print): breaking up creation of each line in display into… 

    … subclasses
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    andreasprlic committed May 28, 2024
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Commits on May 29, 2024

  1. feat(pretty print): breaking up creation of each line in display into… 

    … subclasses
    @andreasprlic
    andreasprlic committed May 29, 2024
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Commits on Jun 1, 2024

  1. feat(pretty print): feat(pretty print): improvements for RNA coding t… 

    …ranscripts, new option to show reverse-chrom strand sequence.
    @andreasprlic
    andreasprlic committed Jun 1, 2024
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Commits on Jun 3, 2024

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

    @andreasprlic
    andreasprlic committed Jun 3, 2024
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  2. feat(repeat-detection): using fully justified representation.

    @andreasprlic
    andreasprlic committed Jun 3, 2024
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  3. formatting

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    andreasprlic committed Jun 3, 2024
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Commits on Jun 6, 2024

  1. feat(prot-pos): now showing the protein (amino acid) positions more c… 

    …learly
    @andreasprlic
    andreasprlic committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. feat(repeat-detection): now with better detection of repetitive units… 

    … that are larger than 1 bp.
    @andreasprlic
    andreasprlic committed Jun 7, 2024
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  2. feat(repeat-detection): hooking repeat detection improvements in pret… 

    …ty print.
    @andreasprlic
    andreasprlic committed Jun 7, 2024
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Commits on Jun 9, 2024

  1. Merge branch 'main' into pretty_print 

    # Conflicts:
#	tests/data/cache-py3.hdp
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    andreasprlic committed Jun 9, 2024
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Commits on Jun 30, 2024

  1. feat(pretty_print): now showing hgvs_p, making code more accessible f… 

    …or consumer
    @andreasprlic
    andreasprlic committed Jun 30, 2024
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  2. Merge branch 'main' of github.com:biocommons/hgvs into pretty_print

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    andreasprlic committed Jun 30, 2024
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  3. feat(ci): trying to get pytest to work again

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    andreasprlic committed Jun 30, 2024
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Commits on Jul 1, 2024

  1. feat(cleanup): removing cache from test_repeats. They are creating to… 

    …o big of a cache.
    @andreasprlic
    andreasprlic committed Jul 1, 2024
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Commits on Aug 13, 2024

  1. cleanup

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    andreasprlic committed Aug 13, 2024
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Commits on Sep 2, 2024

  1. biocommons#741 small refactoring to update directory structure, based… 

    … on PR comments
    @andreasprlic
    andreasprlic committed Sep 2, 2024
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  2. Merge branch 'main' into pretty_print

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    andreasprlic committed Sep 2, 2024
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  3. biocommons#741 small refactoring to update directory structure, based… 

    … on PR comments, also disabling slow running unit test
    @andreasprlic
    andreasprlic committed Sep 2, 2024
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Commits on Sep 6, 2024

  1. biocommons#741 excluding data intensive tests from CI. They would cre… 

    …ate too much caching burden.
    @andreasprlic
    andreasprlic committed Sep 6, 2024
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  2. trying to fix CI

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    andreasprlic committed Sep 6, 2024
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Commits on Sep 7, 2024

  1. feat(repeats): found an issue with count_pattern_occurences, fixed an… 

    …d with more unit tests.
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    andreasprlic committed Sep 7, 2024
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Commits on Sep 16, 2024

  1. feat(repeats): adding examples from HGVS repeats recommendations page… 

    …. Improved repeat analyzer, that now supports 5' and 3' shuffling.
    @andreasprlic
    andreasprlic committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. feat(repeats): adding an example of a large variant to make sure we d… 

    …on't run repeat analysis where it does not make sense. Starting to add support for non-splign alignments.
    @andreasprlic
    andreasprlic committed Sep 17, 2024
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Commits on Sep 19, 2024

  1. feat(repeats): moving max repeat config to global config. Also a smal… 

    …l improvement at the loss of repeat check.
    @andreasprlic
    andreasprlic committed Sep 19, 2024
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  2. skipfeat(repeats): skipping more tests that are too data heavy.

    @andreasprlic
    andreasprlic committed Sep 19, 2024
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  3. feat(repeats): improvements in repeat check.

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    andreasprlic committed Sep 19, 2024
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Commits on Oct 3, 2024

  1. feat(reverse-strand): Now showing reverse strand transcript in 5'-3' … 

    …orientation relative to the transcript by default (can be configured).
    @andreasprlic
    andreasprlic committed Oct 3, 2024
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  2. feat(is_rna): moving the check if a transcript is RNA only to datacom… 

    …piler
    @andreasprlic
    andreasprlic committed Oct 3, 2024
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  3. fix

    @andreasprlic
    andreasprlic committed Oct 3, 2024
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Commits on Nov 16, 2024

  1. fixing off-by one error at transcript start, problematic intergenic v… 

    …ariants, and only one assembly mapper on pretty print.
    @andreasprlic
    andreasprlic committed Nov 16, 2024
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