staar: add metasvm_pred + genehancer columns to annotation parquet#126
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staar: add metasvm_pred + genehancer columns to annotation parquet#126
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) STAARpipeline's coding masks (disruptive_missense, plof_ds, ptv_ds) key off MetaSVM_pred=="D". We carried cadd_phred + revel as proxies, which means our masks don't match R. GeneHancer is an opaque identifier string the pipeline passes through for downstream tooling. Pulls both from FAVOR full-tier (a.dbnsfp.metasvm_pred and a.genehancer.id), flows them end-to-end: ingest -> cohort parquet -> VariantIndexEntry -> AnnotatedVariant -> MetaSTAAR sumstats schema. MetaSVM parses into a typed enum (Deleterious/Tolerated/Unknown) so A3's mask-predicate flip is a pattern match, not a string compare. GeneHancer stays Box<str>; no predicate reads it today. Preflight gains require_structural_annotation_catalog alongside the 11-weight catalog lock from #104. Fails loud at staar start if either column is missing from the cohort, so users with an old cohort get a clear rebuild message. No mask math changes; that's #77.
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Closes #107. STAARpipeline masks disruptive_missense / plof_ds / ptv_ds all key off MetaSVM_pred=="D". We were proxying with cadd_phred + revel, so our masks don't match R. GeneHancer is an opaque ID string the pipeline passes through for downstream tools.
Pulls both from FAVOR full-tier (a.dbnsfp.metasvm_pred, a.genehancer.id) and wires them through ingest -> cohort parquet -> VariantIndexEntry -> AnnotatedVariant -> MetaSTAAR sumstats. MetaSvmPred is a typed enum so A3's mask flip is a pattern match rather than a string compare.
Preflight adds require_structural_annotation_catalog next to the 11-weight lock; old cohorts get a clear rebuild message. No mask math changes yet — that's #77.
cargo test: 294/294, clippy clean.