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Tuple to dataclass - #2

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tuple_to_dataclass

Commits on Feb 19, 2026
- Use hgvs_position_model dataclass for HGVS position results
  Xiaoyun Liu
  committed
  379e565
- Add function to convert from tuple to HGVSPositionModel
  Xiaoyun Liu
  committed
  bbd38da
Commits on Feb 20, 2026
- Refactor(locus):return dict position model and update test
  Xiaoyun Liu
  committed
  5122c55
- Refactor(multi_locus):return dict position model and update test
  Xiaoyun Liu
  committed
  836d7d3
- Fix typo
  Xiaoyun Liu
  committed
  89cdba7
- Refactor(crossmapper): convert Genomic to dict-based position model
  Xiaoyun Liu
  committed
  2d4e2eb
- Refactor(crossmapper): convert NonCoding to dict-based position model
  Xiaoyun Liu
  committed
  923cd9f
- Refactor (locus, multi_locus): allow 'u', 'd' for UTR areas in hgvs model
  Xiaoyun Liu
  committed
  259481b
- Refactor test modules for Genomic and NonCoding
  Xiaoyun Liu
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  55fd346
Commits on Feb 26, 2026
- Remove 'region' in locus position model
  Xiaoyun Liu
  committed
  84127e5
- Refactor(multi_locus): replace tuple with dict
  Xiaoyun Liu
  committed
  eb6ce9b
- Refactor crossmapper and tests, allow ''/*/- in position model for Coding class
  Xiaoyun Liu
  committed
  7d7bc9b
- Refactor(multi_locus): degenerate positions for multi_locus and tests
  Xiaoyun Liu
  committed
  0433303
Commits on Feb 27, 2026
- Refactor(crossmapper): implement hgvs position model for protein and write degenerate in the same flow.
  Xiaoyun Liu
  committed
  a583f00
Commits on Mar 5, 2026
- Refactor(crossmapper): discard degenerate option
  Xiaoyun Liu
  committed
  a57a3e6
- Change examples in README.
  Xiaoyun Liu
  committed
  d245cd6
Commits on Mar 6, 2026
- Discard dataclass object for hgvs position model
  Xiaoyun Liu
  committed
  89559e4
- Refactor(crossmapper): allow degenerate option for 'u' and 'd' area
  Xiaoyun Liu
  committed
  08739ff
Commits on Mar 9, 2026
- Cleanup(locus)
  Xiaoyun Liu
  committed
  fecf026
- Cleanup(multi_locus)
  Xiaoyun Liu
  committed
  54746ec
- Cleanup(multi_locus)
  Xiaoyun Liu
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  5ba6a5a
- Format(multi locus test)
  Xiaoyun Liu
  committed
  7f32afc
- Cleanup(crossmapper): on Genomic and NonCoding
  Xiaoyun Liu
  committed
  e23fe2a
- Cleanup
  Xiaoyun Liu
  committed
  8f05341
Commits on Mar 10, 2026
- Refactor degenerate tests
  Xiaoyun Liu
  committed
  09f721f
- Add position model description for g.,n.,c.,and p.
  Xiaoyun Liu
  committed
  abead48
- Format document
  Xiaoyun Liu
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  b528f92
- Format document
  Xiaoyun Liu
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  6c1b52e
- Format document
  Xiaoyun Liu
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  b871601
- Format document in .rst style
  Xiaoyun Liu
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  9e91d1d
- Format document in .rst style
  Xiaoyun Liu
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  35359b8
- Format and add an example
  Xiaoyun Liu
  committed
  d48f99d
- Add table for Genomic positions and coordinate mapping
  Xiaoyun Liu
  committed
  d16278b
- Format table
  Xiaoyun Liu
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  b29309a
- Format table
  Xiaoyun Liu
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  d1c4c2f
- Format table
  Xiaoyun Liu
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  7966a14
- Add tables
  Xiaoyun Liu
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  035c479
- Fix table syntax
  Xiaoyun Liu
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  f116376
- Fix table syntax
  Xiaoyun Liu
  committed
  89787e6
- Fix table syntax
  Xiaoyun Liu
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  5e601dc
- Fix table syntax
  Xiaoyun Liu
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  751bc3b
- Fix table indent
  Xiaoyun Liu
  committed
  9d156c8
- Update README.rst
  XLIU-hub
  authored
  ebbb90a
- Make scrollable tables in README
  XLIU-hub
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  9ffa9bf
- Update README.rst
  XLIU-hub
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  90f3d71
- Update README.rst
  XLIU-hub
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  93f59ca
- Format table
  Xiaoyun Liu
  committed
  0ef6003
- Use code block for table
  XLIU-hub
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  2704e52
- Update README.rst
  XLIU-hub
  authored
  78183fd
- Refactor: crossmapper and tests for degenerate option
  Xiaoyun Liu
  committed
  03309a8
Commits on Mar 11, 2026
- Add surpport for degenerate position model as input
  Xiaoyun Liu
  committed
  fccc275
- Add degenerate tests
  Xiaoyun Liu
  committed
  00e98bd
- Cleanup
  Xiaoyun Liu
  committed
  e281d64
- Cleanup
  Xiaoyun Liu
  committed
  925cb56
- Local copy before checkout
  Xiaoyun Liu
  committed
  5f2bef7
- Update table for Genomic and NonCoding classes in document
  XLIU-hub
  authored
  55fe797
- Update table for Coding class in document
  XLIU-hub
  authored
  a2003b3
- Add HGVS column in coding table
  XLIU-hub
  authored
  4d9089a
- Fix sytax
  XLIU-hub
  authored
  1542894
- Update protein example in document
  XLIU-hub
  authored
  75a5cba
Commits on Mar 12, 2026
- Add protein table in document
  XLIU-hub
  authored
  b0ed66f
- Fix typo
  XLIU-hub
  authored
  16e9a62
Commits on Mar 13, 2026
- Add tests
  Xiaoyun Liu
  committed
  d6c868d
- Merge branch 'tuple_to_dataclass' of github.com:mutalyzer/crossmapper into tuple_to_dataclass
  Xiaoyun Liu
  committed
  9f24c53
- Refactor crossmap
  Xiaoyun Liu
  committed
  41bd3d5
- Cleanup
  Xiaoyun Liu
  committed
  1752363
- Cleanup
  Xiaoyun Liu
  committed
  31f483a
- Cleanup
  Xiaoyun Liu
  committed
  eeacf85
- Cleanup
  Xiaoyun Liu
  committed
  bb8ee66
- Add missing tests
  Xiaoyun Liu
  committed
  87f507d
- Add missing tests
  Xiaoyun Liu
  committed
  e5d7342
- Refactor
  Xiaoyun Liu
  committed
  53954d3
Commits on Mar 20, 2026
- Cleanup
  Xiaoyun Liu
  committed
  6cb7d32
- Cleanup and add tests
  Xiaoyun Liu
  committed
  3e32bb9
- Update tables in documentation
  XLIU-hub
  authored
  186e2a6
- Update README.rst
  XLIU-hub
  authored
  617b126
- Use single quate for dictionary
  Xiaoyun Liu
  committed
  4fddbc3
- Merge branch 'tuple_to_dataclass' of github.com:mutalyzer/crossmapper into tuple_to_dataclass
  Xiaoyun Liu
  committed
  2c7d005
- Delete table
  XLIU-hub
  authored
  f85b25f
- Update README.rst
  XLIU-hub
  authored
  ca4379e
- Update library, replace tuple with dictionary
  Xiaoyun Liu
  committed
  072719d
- Merge branch 'tuple_to_dataclass' of github.com:mutalyzer/crossmapper into tuple_to_dataclass
  Xiaoyun Liu
  committed
  69c81c2
- Use python code block in library.rst
  XLIU-hub
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  fba6b95
- Update library.rst
  XLIU-hub
  authored
  ca45f67
- Update library.rst
  XLIU-hub
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  e4e1642
- Update library.rst
  XLIU-hub
  authored
  b630851
- Update library.rst
  XLIU-hub
  authored
  a0514c8
- Update library.rst
  XLIU-hub
  authored
  21ce8dd
- Update library.rst
  XLIU-hub
  authored
  6fc7709
- Update library.rst
  XLIU-hub
  authored
  1693bab
- Add backticks
  Xiaoyun Liu
  committed
  9bb4501
- Merge branch 'tuple_to_dataclass' of github.com:mutalyzer/crossmapper into tuple_to_dataclass
  Xiaoyun Liu
  committed
  9ceea41
- Cleanup
  Xiaoyun Liu
  committed
  691ec35
- Cleanup, use '' in dictionary
  Xiaoyun Liu
  committed
  bcf7bd2
- Cleanup, use typings
  Xiaoyun Liu
  committed
  2f167e0
Commits on Mar 23, 2026
- Cleanup
  Xiaoyun Liu
  committed
  ac0cd16
- Cleanup
  Xiaoyun Liu
  committed
  2ebf6c9
- Stop trackinhg local file
  Xiaoyun Liu
  committed
  f2e8efa
- Delete tmp files from branch
  Xiaoyun Liu
  committed
  4e6443c
- Cleanup
  Xiaoyun Liu
  committed
  8deedc1
- Refactor protein conversion
  Xiaoyun Liu
  committed
  f5f7a51
- Add degenerate tests
  Xiaoyun Liu
  committed
  79cbcc0
- Add backticks for region in table
  Xiaoyun Liu
  committed
  1459451
- Cleanup
  Xiaoyun Liu
  committed
  e92c78e
Commits on Mar 25, 2026
- Discard normalize position model
  Xiaoyun Liu
  committed
  f810567
- Fix test
  Xiaoyun Liu
  committed
  c5d7732
Commits on Mar 26, 2026
- Add degenerate for NonCoding
  Xiaoyun Liu
  committed
  49ecb5f
- Add tests for degenerate in NonCoding
  Xiaoyun Liu
  committed
  7849195
- Update document
  Xiaoyun Liu
  committed
  7c3cdde
- Formatting
  Xiaoyun Liu
  committed
  651d170
- Update library.rst
  XLIU-hub
  authored
  21f8458
- Fix typo
  Xiaoyun Liu
  committed
  34d0844
- Update .gitignore
  XLIU-hub
  authored
  8873a77
Commits on Mar 27, 2026
- Set upstream and downstream in multilocus as 0 based
  Xiaoyun Liu
  committed
  c9e58c6
- Fix typing mistake
  Xiaoyun Liu
  committed
  783223d
- Use importlib instead of pkg_resources
  XLIU-hub
  authored
  a7196f4
Commits on Mar 30, 2026
- Fix typing and single quote
  Xiaoyun Liu
  committed
  88ce74f
- Fix doc string
  Xiaoyun Liu
  committed
  6d5e282
- Update python version in setup
  Xiaoyun Liu
  committed
  8fba978
- Rename multilocus positon model
  Xiaoyun Liu
  committed
  2867ea8
- Remove unneccessary elif
  Xiaoyun Liu
  committed
  12229cd
- Fix flake8 whitespace issues
  Xiaoyun Liu
  committed
  c6455e9
- Fix whitespaces
  Xiaoyun Liu
  committed
  12e8e1f
- Add tests for protein positions from the reverse strand
  Xiaoyun Liu
  committed
  e2f2a43
Commits on Mar 31, 2026
- Rename external (input/output) variable to pos_m and add test for a one base intron in coding
  Xiaoyun Liu
  committed
  50d50b5
- Fix typo and font
  Xiaoyun Liu
  committed
  73e2965
Commits on Apr 1, 2026
- Update degenerate for noncoding and tests
  Xiaoyun Liu
  committed
  3ec8ab4
- Update degenerate for noncoding example in documentation
  Xiaoyun Liu
  committed
  ba091d5
- Discard unneccessary functions for coding
  Xiaoyun Liu
  committed
  39d1d6b
- Cleanup
  Xiaoyun Liu
  committed
  915e845
- Fix error for inverted coding
  Xiaoyun Liu
  committed
  69eb985
Commits on May 7, 2026
- Treat upstream and downstream as introns.
  Xiaoyun Liu
  committed
  c08b52b
Commits on May 8, 2026
- Local change before swith branch
  Xiaoyun Liu
  committed
  87818ca
- Local change before swith branch
  Xiaoyun Liu
  committed
  917d509
Commits on May 11, 2026
- Implement changes in upstream and downstream, degenerate option; add tests
  Xiaoyun Liu
  committed
  e205144
- Update documentation for upstream and downstream regions
  Xiaoyun Liu
  committed
  07c537b
Commits on May 12, 2026
- Reshape outputs from downstream regions and add tests.
  Xiaoyun Liu
  committed
  3f18bdb
Commits on May 13, 2026
- Add tests for degenerate return in small UTR regions
  Xiaoyun Liu
  committed
  f73893c
Commits on May 26, 2026
- Formatting according to pylint
  Xiaoyun Liu
  committed
  6cc6f5a
- Formatting.
  Xiaoyun Liu
  committed
  ebd0cd3
- Remove git conflict.
  Xiaoyun Liu
  committed
  562d7b8
- Discard local variable for degenerate and handle '*' explicitly.
  Xiaoyun Liu
  committed
  136bb18
- Fix typo in tests.
  Xiaoyun Liu
  committed
  327c7dd
Commits on May 27, 2026
- Formatting locus module.
  Xiaoyun Liu
  committed
  67f7242
- Formatting and renaming local variables.
  Xiaoyun Liu
  committed
  b4f3f84
- Crossmapper:Formatting and renaming local variables.
  Xiaoyun Liu
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  d4aea66
Commits on May 29, 2026
- Rename function to_position to to_point and add whitespace around = in typed params.
  Xiaoyun Liu
  committed
  935bbdb
- Undo rename from to_position to to_point and update format.
  Xiaoyun Liu
  committed
  a20096d
- Formatting
  Xiaoyun Liu
  committed
  910c291
Commits on Jun 12, 2026
- Add genomic, noncoding, coding and protein dataclasses
  Xiaoyun Liu
  committed
  d8e7834
- Remove tests values for noncoding degenerate.
  Xiaoyun Liu
  committed
  34d0c9a
Commits on Jun 19, 2026
- Add dataclass internally.
  Xiaoyun Liu
  committed
  ff5c8b5
- Update error raise, add dataclass serialization and use single quate.
  Xiaoyun Liu
  committed
  cfb9107
- Update to use dataclass, add a return in Coding class to avoid intermediate negative position value in degenerate.
  Xiaoyun Liu
  committed
  dc93f87
- Use dataclass point as the basic unit.
  Xiaoyun Liu
  committed
  5cc99a8
- Update tests to use dataclass.
  Xiaoyun Liu
  committed
  4be2bc3
- Formatting.
  Xiaoyun Liu
  committed
  157b92f
Commits on Jun 23, 2026
- Update docstring.
  Xiaoyun Liu
  committed
  dc418ee
- multi_locus: update docstring for dataclass usage.
  Xiaoyun Liu
  committed
  132533b
- test_models: Add tests for dataclass models.
  Xiaoyun Liu
  committed
  c8b4e66
- Update models and use Point dataclass when use locus/multilocus modules.
  Xiaoyun Liu
  committed
  a6d8393
Commits on Jun 24, 2026
- Move dataclass from models to locus and crossmapper.
  Xiaoyun Liu
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  b4aae45
- Correct import.
  Xiaoyun Liu
  committed
  1ac6274
Commits on Jun 25, 2026
- Fix typing error and add test in CI.
  Xiaoyun Liu
  committed
  7bbabe4
- Test importlib_metadata to avoid mypy error from python v3.10 and v3.11.
  Xiaoyun Liu
  committed
  08f2261
Commits on Jul 1, 2026
- Discard redundant checking and overwrite serialization for ProteinPoint.
  Xiaoyun Liu
  committed
  a9fdf97
Commits on Jul 7, 2026
- Use back metadata in importlib.
  Xiaoyun Liu
  committed
  a912455
- Multi_locus: Add checks to validate input coordinate and input point.
  Xiaoyun Liu
  committed
  cc65a7b
Commits on Jul 17, 2026
- Locus.py: Add checks.
  Xiaoyun Liu
  committed
  d2200e3
Commits on Aug 14, 2026
- Add checks in locus module.
  Xiaoyun Liu
  committed
  d10f1b8
- Add checks in multi_locus module.
  Xiaoyun Liu
  committed
  7aa63cc
Commits on Aug 18, 2026
- Move checks from checker to locus module.
  Xiaoyun Liu
  committed
  b0f40c6
- Cleanup.
  Xiaoyun Liu
  committed
  af7f7f7
- Delete checker module and place checks parsely.
  Xiaoyun Liu
  committed
  315c9e3
- Change locus length to one based.
  Xiaoyun Liu
  committed
  692b9bd
- Add checks in multi_locus module and its tests.
  Xiaoyun Liu
  committed
  c432129
- Rephrase error message.
  Xiaoyun Liu
  committed
  c3c4984
Commits on Aug 19, 2026
- Add Coord, multi_locus Point dataclass.
  Xiaoyun Liu
  committed
  a188472
- Update documentation.
  Xiaoyun Liu
  committed
  30a2bb1
- Move Corrd into locus.
  Xiaoyun Liu
  committed
  e9a99a5
- WIP: Add checks in crossmaper and tests.
  Xiaoyun Liu
  committed
  e748ef5
- WIP: Add checks in crossmaper and tests.
  Xiaoyun Liu
  committed
  374ae43
- Fix test.
  Xiaoyun Liu
  committed
  eff9152
- Fix test.
  Xiaoyun Liu
  committed
  8f47500
- Fix typings.
  Xiaoyun Liu
  committed
  d109d17
Commits on Aug 21, 2026
- Fix use PackageMetadata indexing instead of get.
  Xiaoyun Liu
  committed
  d997766
- Remove --strict from mypy.
  Xiaoyun Liu
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  ede43a4
Commits on Aug 24, 2026
- Add checks for upstream and downstream region.
  Xiaoyun Liu
  committed
  fe5c132
Commits on Aug 25, 2026
- Add type checks in locus and implement tests for checks in multi locus module.
  Xiaoyun Liu
  committed
  47e721b
Commits on Aug 26, 2026
- Add tests for checks in noncoding and coding.
  Xiaoyun Liu
  committed
  452856d
- Fix offset checks in upstream and downstream.
  Xiaoyun Liu
  committed
  946e7c4
- Fix offset checks in upstream and downstream.
  Xiaoyun Liu
  committed
  57ae3cc
Commits on Aug 27, 2026
- test_locus: Detailed error message.
  Xiaoyun Liu
  committed
  8f0fdfb
- Locus: Update docstring.
  Xiaoyun Liu
  committed
  c8e07ac
- terst_locus: style according to flake8 formatting.
  Xiaoyun Liu
  committed
  3ca68c2
Commits on Aug 28, 2026
- test_multi_locus: Detailed error message.
  Xiaoyun Liu
  committed
  875d324
- test_crossmapper: Detailed error message.
  Xiaoyun Liu
  committed
  92d9c56
Commits on Aug 31, 2026
- Fix typings and use -offset for negative offset instead of absolute value.
  Xiaoyun Liu
  committed
  f673099
- Fix typing.
  Xiaoyun Liu
  committed
  3aa854e
- Multi_locus:Discard of absolute when validate point.
  Xiaoyun Liu
  committed
  26680c5
- Discard absolute in crossmapper module and add test for protein dataclass invalid intialization.
  Xiaoyun Liu
  committed
  4ce9772
- Discard absolute in crossmapper module and add test for protein dataclass invalid intialization.
  Xiaoyun Liu
  committed
  0778fea
- Use '' for string.
  Xiaoyun Liu
  committed
  127b46b
- Style according to PEP8.
  Xiaoyun Liu
  committed
  68c5718
- Style according to pylint.
  Xiaoyun Liu
  committed
  f84410e
- Style according to pylint.
  Xiaoyun Liu
  committed
  85a5003
- Update error message.
  Xiaoyun Liu
  committed
  69205d8
Commits on Sep 1, 2026
- Style according to pylint.
  Xiaoyun Liu
  committed
  7736997
- Fix typings.
  Xiaoyun Liu
  committed
  2d113c0
Commits on Sep 2, 2026
- Use '' for string.
  Xiaoyun Liu
  committed
  f371e05
- Use '' in string in tests.
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  e4b1859
Commits on Sep 4, 2026
- Remove redundant object inheritance.
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  7d99daf
- Add explicit exception chaining.
  mihailefter
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  193373b
- Allow half-open location ends to equal reference length.
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  0880ed4
- Validate length as a positive integer only.
  mihailefter
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  8eed9dc
- Fix downstream boundary validation when the 3' UTR is missing.
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  25dda81
- Export Coord and Point from the package root.
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  3f06bbf
- Drop the unused pytest-pep8 configuration and dependency.
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  4976c30
- Swaph the length and inverted parameters.
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  6b2b792
Commits on Sep 5, 2026
- Correct degenerate also in protein to coordinate.
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  03adc65
- Distinguish out of order loci from overlapping ones.
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  73d9827
Commits on Sep 6, 2026
- Remove the Coord dataclass and switch back to plain integers for coordinates.
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  committed
  58f3f0f
- Reject negative coordinates and document the locus module.
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  committed
  0a1dbdd
Commits on Sep 8, 2026
- Document the multi locus module and remove types from docstrings.
  mihailefter
  committed
  43c5ccb
Commits on Sep 9, 2026
- Remove types from docs.
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  7daf35b
- Document the crossmapper module.
  mihailefter
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  faf89df
- Reject unsupported types for the orientation and the position in codon.
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  1fda7b8
Commits on Sep 10, 2026
- Be more specific when checking the CDS.
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  5326b00
- Accept downstream position 1 only when it can be converted.
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  c789c96
- Report a degenerate position beyond the sequence as written.
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  aa4a78a
- No more reference.
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  36ae407
- Fix the documentation examples and run them automatically.
  mihailefter
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  57cf6da
- Let each class in the hierarchy check only what it owns.
  mihailefter
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  98846c4
- Stop recomputing what Locus already does.
  mihailefter
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  165c7bf
- Simplify multi locus point validation.
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  a0ffafc
Commits on Sep 11, 2026
- Ask the MultiLocus for its length instead of deriving it.
  mihailefter
  committed
  ca6df6a
Commits on Sep 15, 2026
- Specify allowed position values in upstream.
  Xiaoyun Liu
  committed
  36d24e4
- Fix typing error.
  Xiaoyun Liu
  committed
  192f829
- Cleanup.
  Xiaoyun Liu
  committed
  d7f6782
Commits on Sep 16, 2026
- Assign constant value in downstream regardless of missing 3'UTR.
  Xiaoyun Liu
  committed
  b57871a

Commits

Commits on Feb 19, 2026

Commits on Feb 20, 2026

Commits on Feb 26, 2026

Commits on Feb 27, 2026

Commits on Mar 5, 2026

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