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VCF support for RLE and fix to same-as-reference allele normalization to RLE - #589

Merged

theferrit32 merged 42 commits into

mainfrom

issue-577-VCF-RLE

Dec 15, 2025

Merged

VCF support for RLE and fix to same-as-reference allele normalization to RLE#589
theferrit32 merged 42 commits into
mainfrom
issue-577-VCF-RLE

Commits on Oct 15, 2025
- Initial revision of ReferenceLengthExpression in VCF annotator
  theferrit32
  committed
  6b36ba1
- No longer need FieldName.default_value since we can rely on pysam
  theferrit32
  committed
  76cd565
Commits on Oct 16, 2025
- Fix INFO field setting to allow 0 for Integers.
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  committed
  4f22083
- Reworking the RLE flow
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  committed
  94cc277
- Move around code some more
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  committed
  d048501
Commits on Oct 22, 2025
- Adding some tests
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  committed
  6051b11
Commits on Nov 11, 2025
- Add more RLE test cases
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  committed
  c627c50
- Fix test_allele_translator for RLE NC_000013.11:g.32936732=
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  committed
  499002e
Commits on Nov 12, 2025
- remove id/digest testing from allele test
  theferrit32
  committed
  4db6c3c
- Fix test_annotate_vcf_grch38_noattrs with ref alleles
  theferrit32
  committed
  3e121be
- Update incorrect ref allele test case. Refresh expected VCFs
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  committed
  eac0dc5
- Refresh tests/cassettes/test_normalize_allele.yaml
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  committed
  491de1b
- Update comment
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  b1a7b5f
- Change test VCFs to uncompressed text so diffs can be seen going forwards.
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  committed
  bce957a
- Include sequence value in output vcf if the length of that sequence is <= MAX_LITERAL_STATE_LENGTH, defaulted to 15
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  committed
  c0042c3
- Remove commented blocks
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  committed
  6df2ba2
- Update test name
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  committed
  460d6bb
- Add comments to cases in test_vrs_normalize.py
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  committed
  b7fa124
- Add make target clean-cassettes
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  committed
  576e4db
- Minor tweak to all_played checks in vcf annotator tests to make re-recording easier
  theferrit32
  committed
  70bd6e2
- Ignore VRS and Python version header values in VCF tests
  theferrit32
  committed
  adf5f73
Commits on Nov 13, 2025
- Add missing cassette
  theferrit32
  committed
  2c5c1dd
- Don't fail test when vcr is being rewritten. Refresh cassettes
  theferrit32
  committed
  9a65b82
- add decode_compressed_response=True to vcr config
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  committed
  94ad735
- Add vcr_config to conftest.py. Delete vcr_support.py. Refresh cassettes
  theferrit32
  committed
  7723d5c
Commits on Nov 17, 2025
- Merge remote-tracking branch 'origin/main' into issue-577-VCF-RLE
  theferrit32
  committed
  6255779
Commits on Nov 18, 2025
- Reset casettes for RLE tests after merge from main
  theferrit32
  committed
  26eeba3
Commits on Nov 20, 2025
- Adding microsatellite RLE cases
  theferrit32
  committed
  c8282c2
- Make (incorrect) changes to normalize same-as-ref RLE variants
  theferrit32
  committed
  97a583c
Commits on Nov 26, 2025
- Do not normalize same-as-ref. Further refactoring and documentation in _normalize_allele. More tests
  theferrit32
  committed
  6a442c9
Commits on Dec 2, 2025
Commits on Dec 3, 2025
- Fix VCF annotations to match source changes
  theferrit32
  committed
  aed34f1
- Clean up error in cassette
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  committed
  44af087
Commits on Dec 12, 2025
- Remove unused vrs_data_key
  theferrit32
  committed
  77cb9c7
- Update vcf.py to replace MAX_LITERAL_STATE_LENGTH with a RLE_SEQ_LIMIT specific to RLE that defaults to 50, and excludes sequence vals from INFO if over that
  theferrit32
  committed
  f3ce393
- Apply suggestions from code review
  
  theferrit32
  and
  korikuzma
  authored
  83f9296
- Use enumerated sequence types in vcf.py
  theferrit32
  committed
  a52ec24
- Update src/ga4gh/vrs/normalize.py
  
  theferrit32
  and
  korikuzma
  authored
  938e3e0
- Fix formatting
  theferrit32
  committed
  2234438

Commits

Commits on Oct 15, 2025

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Commits on Nov 26, 2025

Commits on Dec 2, 2025

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Commits on Dec 12, 2025