Code

feat(#741): Pretty print#742

Code

Open

andreasprlic wants to merge 33 commits intobiocommons:mainbiocommons/hgvs:mainfrom andreasprlic:pretty_printandreasprlic/hgvs:pretty_printCopy head branch name to clipboard

+2,891-3

Commits

Commits on May 13, 2024

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

  andreasprlic

  committed
  c254b47

  Copy full SHA for c254b47

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

  andreasprlic

  committed
  8986d20

  Copy full SHA for 8986d20

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

  andreasprlic

  committed
  e9fde79

  Copy full SHA for e9fde79

Commits on May 28, 2024

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

  andreasprlic

  committed
  d3a5e6e

  Copy full SHA for d3a5e6e

Commits on May 29, 2024

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

  andreasprlic

  committed
  f2018df

  Copy full SHA for f2018df

Commits on Jun 1, 2024

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

  andreasprlic

  committed
  2f7069b

  Copy full SHA for 2f7069b

Commits on Jun 3, 2024

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

  andreasprlic

  committed
  27ae2cd

  Copy full SHA for 27ae2cd

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

  andreasprlic

  committed
  b5b3d64

  Copy full SHA for b5b3d64

• formatting

  andreasprlic

  committed
  2a72299

  Copy full SHA for 2a72299

Commits on Jun 6, 2024

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

  andreasprlic

  committed
  0dcab28

  Copy full SHA for 0dcab28

Commits on Jun 7, 2024

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

  andreasprlic

  committed
  e9f578a

  Copy full SHA for e9f578a

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

  andreasprlic

  committed
  99a614f

  Copy full SHA for 99a614f

Commits on Jun 9, 2024

• Merge branch 'main' into pretty_print

  Show description for da48e01
  andreasprlic

  committed
  da48e01

  Copy full SHA for da48e01

Commits on Jun 30, 2024

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

  andreasprlic

  committed
  f1e9703

  Copy full SHA for f1e9703

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

  andreasprlic

  committed
  7ad7f0c

  Copy full SHA for 7ad7f0c

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

  andreasprlic

  committed
  a31cd26

  Copy full SHA for a31cd26

Commits on Jul 1, 2024

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

  andreasprlic

  committed
  30addf2

  Copy full SHA for 30addf2

Commits on Aug 13, 2024

• cleanup

  andreasprlic

  committed
  bc483b5

  Copy full SHA for bc483b5

Commits on Sep 2, 2024

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

  andreasprlic

  committed
  cf22aae

  Copy full SHA for cf22aae

• Merge branch 'main' into pretty_print

  andreasprlic

  committed
  d4f2ac4

  Copy full SHA for d4f2ac4

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

  andreasprlic

  committed
  d08f02d

  Copy full SHA for d08f02d

Commits on Sep 6, 2024

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

  andreasprlic

  committed
  401c5a3

  Copy full SHA for 401c5a3

• trying to fix CI

  andreasprlic

  committed
  336ea2c

  Copy full SHA for 336ea2c

Commits on Sep 7, 2024

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

  andreasprlic

  committed
  d216bba

  Copy full SHA for d216bba

Commits on Sep 16, 2024

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

  andreasprlic

  committed
  9d15a22

  Copy full SHA for 9d15a22

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.

  andreasprlic

  committed
  99f27bf

  Copy full SHA for 99f27bf

Commits on Sep 19, 2024

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

  andreasprlic

  committed
  703efbf

  Copy full SHA for 703efbf

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

  andreasprlic

  committed
  bb7eb3c

  Copy full SHA for bb7eb3c

• feat(repeats): improvements in repeat check.

  andreasprlic

  committed
  fed5af4

  Copy full SHA for fed5af4

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).

  andreasprlic

  committed
  9a2e049

  Copy full SHA for 9a2e049

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

  andreasprlic

  committed
  b82ab35

  Copy full SHA for b82ab35

• fix

  andreasprlic

  committed
  cdd87a5

  Copy full SHA for cdd87a5

Commits on Nov 16, 2024

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

  andreasprlic

  committed
  9a77892

  Copy full SHA for 9a77892