Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat(#741): Pretty print #742

Open
wants to merge 32 commits into
base: main
Choose a base branch
from
Open

feat(#741): Pretty print #742

wants to merge 32 commits into from

Commits on May 13, 2024

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

    … hgvs variants.
    @andreasprlic
    andreasprlic committed May 13, 2024
    Configuration menu
    Copy the full SHA
    c254b47 View commit details
    Browse the repository at this point in the history

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

    @andreasprlic
    andreasprlic committed May 13, 2024
    Configuration menu
    Copy the full SHA
    8986d20 View commit details
    Browse the repository at this point in the history

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

    @andreasprlic
    andreasprlic committed May 13, 2024
    Configuration menu
    Copy the full SHA
    e9fde79 View commit details
    Browse the repository at this point in the history

Commits on May 28, 2024

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

    … subclasses
    @andreasprlic
    andreasprlic committed May 28, 2024
    Configuration menu
    Copy the full SHA
    d3a5e6e View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    f2018df View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    2f7069b View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2024

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

    @andreasprlic
    andreasprlic committed Jun 3, 2024
    Configuration menu
    Copy the full SHA
    27ae2cd View commit details
    Browse the repository at this point in the history

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

    @andreasprlic
    andreasprlic committed Jun 3, 2024
    Configuration menu
    Copy the full SHA
    b5b3d64 View commit details
    Browse the repository at this point in the history

  3. formatting

    @andreasprlic
    andreasprlic committed Jun 3, 2024
    Configuration menu
    Copy the full SHA
    2a72299 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    0dcab28 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    e9f578a View commit details
    Browse the repository at this point in the history

  2. feat(repeat-detection): hooking repeat detection improvements in pret… 

    …ty print.
    @andreasprlic
    andreasprlic committed Jun 7, 2024
    Configuration menu
    Copy the full SHA
    99a614f View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2024

  1. Merge branch 'main' into pretty_print 

    # Conflicts:
#	tests/data/cache-py3.hdp
    @andreasprlic
    andreasprlic committed Jun 9, 2024
    Configuration menu
    Copy the full SHA
    da48e01 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    f1e9703 View commit details
    Browse the repository at this point in the history

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

    @andreasprlic
    andreasprlic committed Jun 30, 2024
    Configuration menu
    Copy the full SHA
    7ad7f0c View commit details
    Browse the repository at this point in the history

  3. feat(ci): trying to get pytest to work again

    @andreasprlic
    andreasprlic committed Jun 30, 2024
    Configuration menu
    Copy the full SHA
    a31cd26 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    30addf2 View commit details
    Browse the repository at this point in the history

Commits on Aug 13, 2024

  1. cleanup

    @andreasprlic
    andreasprlic committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    bc483b5 View commit details
    Browse the repository at this point in the history

Commits on Sep 2, 2024

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

    … on PR comments
    @andreasprlic
    andreasprlic committed Sep 2, 2024
    Configuration menu
    Copy the full SHA
    cf22aae View commit details
    Browse the repository at this point in the history

  2. Merge branch 'main' into pretty_print

    @andreasprlic
    andreasprlic committed Sep 2, 2024
    Configuration menu
    Copy the full SHA
    d4f2ac4 View commit details
    Browse the repository at this point in the history

  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
    Configuration menu
    Copy the full SHA
    d08f02d View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    401c5a3 View commit details
    Browse the repository at this point in the history

  2. trying to fix CI

    @andreasprlic
    andreasprlic committed Sep 6, 2024
    Configuration menu
    Copy the full SHA
    336ea2c View commit details
    Browse the repository at this point in the history

Commits on Sep 7, 2024

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

    …d with more unit tests.
    @andreasprlic
    andreasprlic committed Sep 7, 2024
    Configuration menu
    Copy the full SHA
    d216bba View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    9d15a22 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    99f27bf View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    703efbf View commit details
    Browse the repository at this point in the history

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

    @andreasprlic
    andreasprlic committed Sep 19, 2024
    Configuration menu
    Copy the full SHA
    bb7eb3c View commit details
    Browse the repository at this point in the history

  3. feat(repeats): improvements in repeat check.

    @andreasprlic
    andreasprlic committed Sep 19, 2024
    Configuration menu
    Copy the full SHA
    fed5af4 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    9a2e049 View commit details
    Browse the repository at this point in the history

  2. feat(is_rna): moving the check if a transcript is RNA only to datacom… 

    …piler
    @andreasprlic
    andreasprlic committed Oct 3, 2024
    Configuration menu
    Copy the full SHA
    b82ab35 View commit details
    Browse the repository at this point in the history

  3. fix

    @andreasprlic
    andreasprlic committed Oct 3, 2024
    Configuration menu
    Copy the full SHA
    cdd87a5 View commit details
    Browse the repository at this point in the history