feat: symbolic-allele-aware ILEN#52

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d-laub merged 24 commits into

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worktree-test-vcfix

Jun 5, 2026

Commits on Jun 5, 2026

docs: design spec for symbolic-allele-aware ILEN

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docs: implementation plan for symbolic-allele-aware ILEN

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feat(exprs): symbolic_ilen helper + is_imprecise expression

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test(exprs): multi-ALT symbolic_ilen regression test + docs

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test(fixtures): add symbolic SV builder for ILEN tests

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test(fixtures): clarify CNV docstring + assert un-sizable records

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test(oracle): expected_ilen helper from GroundTruth

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test(oracle): mirror symbolic_ilen IMPRECISE + END-fallback semantics

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test(oracle): normalize compound SV types; drop unreachable END arm

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feat(vcf): size symbolic SVs via SVLEN/END; persist corrected ILEN

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fix(vcf): don't leak SV INFO placeholder cols; guard ILEN concat alignment

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fix(vcf): restrict INFO header detection to INFO; strengthen ILEN alignment guard

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fix(ilen): coerce null ILEN to 0 at numpy materialization boundaries

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fix(svar): coerce null ILEN to 0 in with-length read + overlap; test lazy/svar paths

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test(ilen): drop tautological assertion; document load-bearing fill_null
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test: symbolic INV fixture row + is_symbolic/is_imprecise filter parity

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test: clarify inert filter callable in parity test
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feat(pgen): size symbolic SVs from PVAR INFO (SVLEN/END)

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docs(pgen): document IMPRECISE flag regex intent
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test(svar): inherits corrected symbolic ILEN from source

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test: property test symbolic ILEN against vcfixture oracle

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docs(skill): document symbolic ILEN, is_imprecise, filter guidance

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fix(exprs): is_snp/is_indel exclude null-ILEN symbolic SVs; test END fallback

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test(pgen): filter parity for ~is_symbolic / ~is_imprecise on symbolic PGEN

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feat: symbolic-allele-aware ILEN#52

feat: symbolic-allele-aware ILEN#52
d-laub merged 24 commits into
mainfrom
worktree-test-vcfix

Commits on Jun 5, 2026

docs: design spec for symbolic-allele-aware ILEN

docs: implementation plan for symbolic-allele-aware ILEN

feat(exprs): symbolic_ilen helper + is_imprecise expression

test(exprs): multi-ALT symbolic_ilen regression test + docs

test(fixtures): add symbolic SV builder for ILEN tests

test(fixtures): clarify CNV docstring + assert un-sizable records

test(oracle): expected_ilen helper from GroundTruth

test(oracle): mirror symbolic_ilen IMPRECISE + END-fallback semantics

test(oracle): normalize compound SV types; drop unreachable END arm

feat(vcf): size symbolic SVs via SVLEN/END; persist corrected ILEN

fix(vcf): don't leak SV INFO placeholder cols; guard ILEN concat alignment

fix(vcf): restrict INFO header detection to INFO; strengthen ILEN alignment guard

fix(ilen): coerce null ILEN to 0 at numpy materialization boundaries

fix(svar): coerce null ILEN to 0 in with-length read + overlap; test lazy/svar paths

test(ilen): drop tautological assertion; document load-bearing fill_null

test: symbolic INV fixture row + is_symbolic/is_imprecise filter parity

test: clarify inert filter callable in parity test

feat(pgen): size symbolic SVs from PVAR INFO (SVLEN/END)

docs(pgen): document IMPRECISE flag regex intent

test(svar): inherits corrected symbolic ILEN from source

test: property test symbolic ILEN against vcfixture oracle

docs(skill): document symbolic ILEN, is_imprecise, filter guidance

fix(exprs): is_snp/is_indel exclude null-ILEN symbolic SVs; test END fallback

test(pgen): filter parity for ~is_symbolic / ~is_imprecise on symbolic PGEN