feat(cli): replace --skip-symbolic-alts with composable --no-symbolic / --no-breakend#53

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feat/breakend-alts

Jun 5, 2026

Commits on Jun 5, 2026

feat(exprs): add is_breakend; treat breakend ALTs as un-sizable (null ILEN)

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docs(spec): SVAR write CLI symbolic + breakend filter flags

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docs(plan): SVAR write CLI symbolic + breakend filter flags

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feat(exprs): add record-level _record_is_symbolic/_record_is_breakend predicates

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feat(cli): replace --skip-symbolic-alts with --no-symbolic and --no-breakend

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test(cli): use no_symbolic in renamed-flag CLI tests

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test(cli): add breakend + combined-flag SVAR write tests

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test(cli): add combined/no-flag PGEN tests; rename no_symbolic CLI tests

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feat(vcf): enforce filter/pl_filter pair invariant in VCF.filter setter

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