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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

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issue-577-VCF-RLE

Dec 15, 2025

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.
theferrit32
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4f22083
Reworking the RLE flow
theferrit32
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94cc277
Move around code some more
theferrit32
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d048501

Commits on Oct 22, 2025

Adding some tests
theferrit32
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6051b11

Commits on Nov 11, 2025

Add more RLE test cases
theferrit32
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c627c50
Fix test_allele_translator for RLE NC_000013.11:g.32936732=
theferrit32
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499002e

Commits on Nov 12, 2025

remove id/digest testing from allele test
theferrit32
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4db6c3c
Fix test_annotate_vcf_grch38_noattrs with ref alleles
theferrit32
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3e121be
Update incorrect ref allele test case. Refresh expected VCFs
theferrit32
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eac0dc5
Refresh tests/cassettes/test_normalize_allele.yaml
theferrit32
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491de1b
Update comment
theferrit32
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b1a7b5f
Change test VCFs to uncompressed text so diffs can be seen going forwards.
theferrit32
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bce957a
Include sequence value in output vcf if the length of that sequence is <= MAX_LITERAL_STATE_LENGTH, defaulted to 15
theferrit32
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c0042c3
Remove commented blocks
theferrit32
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6df2ba2
Update test name
theferrit32
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460d6bb
Add comments to cases in test_vrs_normalize.py
theferrit32
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b7fa124
Add make target clean-cassettes
theferrit32
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576e4db
Minor tweak to all_played checks in vcf annotator tests to make re-recording easier
theferrit32
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70bd6e2
Ignore VRS and Python version header values in VCF tests
theferrit32
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adf5f73

Commits on Nov 13, 2025

Commits on Nov 17, 2025

Merge remote-tracking branch 'origin/main' into issue-577-VCF-RLE
theferrit32
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6255779

Commits on Nov 18, 2025

Reset casettes for RLE tests after merge from main
theferrit32
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26eeba3

Commits on Nov 20, 2025

Adding microsatellite RLE cases
theferrit32
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c8282c2
Make (incorrect) changes to normalize same-as-ref RLE variants
theferrit32
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97a583c

Commits on Nov 26, 2025

Do not normalize same-as-ref. Further refactoring and documentation in _normalize_allele. More tests
theferrit32
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6a442c9

Commits on Dec 3, 2025

Fix VCF annotations to match source changes
theferrit32
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aed34f1
Clean up error in cassette
theferrit32
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44af087

Commits on Dec 12, 2025

Remove unused vrs_data_key
theferrit32
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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
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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