changedInput schema / properties / variants / items / description
Previous value: -"Variant ID — chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) or an rsID (rs11591147). Obtain a variantId from ensembl_predict_variant or a VCF. Malformed IDs are reported per-item in failed[], not rejected wholesale."New value: +"Variant ID — chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) on chromosome 1–22, X, or Y with an optional chr prefix, or an rsID (rs11591147). Mitochondrial IDs (M, MT, chrM) are not served. Obtain a variantId from ensembl_predict_variant or a VCF. Malformed IDs are reported per-item in failed[], not rejected wholesale."
changedOutput schema / properties / error / properties / data / properties / reason / description
Previous value: -"Machine-readable failure mode. Declared by this tool: `incoherent_build`: reference_genome was supplied but does not match the dataset. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_variant_id`: A variant ID is outside the chrom-pos-ref-alt or rsID grammar; reported per item in failed[]. `variant_not_found`: A well-formed ID is absent from the requested dataset; reported per item in failed[]. `mitochondrial_unsupported`: A variant ID names the mitochondrial chromosome (M, MT, or chrM); reported per item in failed[]. `ambiguous_rsid`: An rsID maps to more than one variant in the dataset; reported per item in failed[]. `graphql_error`: gnomAD rejected the lookup for one ID with a GraphQL error; reported per item in failed[]. `upstream_build_mismatch`: gnomAD answered one ID with a variant on a different reference build; reported per item in failed[]. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry for one ID; reported per item in failed[]. `upstream_timeout`: Every attempt to reach gnomAD for one ID timed out; reported per item in failed[]. `upstream_access`: gnomAD refused the request for one ID (access denied); reported per item in failed[]. `invalid_upstream_response`: gnomAD kept answering one ID with a response that failed validation; reported per item in failed[]. Other values are possible when a failure originates below the handler."
changedOutput schema / properties / error / properties / data / properties / reason / examples
Previous value: -[
- "incoherent_build"
-]New value: +[
+ "incoherent_build",
+ "invalid_variant_id",
+ "variant_not_found",
+ "mitochondrial_unsupported",
+ "ambiguous_rsid",
+ "graphql_error",
+ "upstream_build_mismatch",
+ "upstream_unavailable",
+ "upstream_timeout",
+ "upstream_access",
+ "invalid_upstream_response"
+]
changedOutput schema / properties / failed / description
Previous value: -"Per-item failures: malformed IDs, variants absent from the dataset, or upstream errors."New value: +"Per-item failures, in input order: malformed IDs, variants absent from the dataset, or upstream errors — each with its reason and recovery hint."
changedOutput schema / properties / failed / items / description
Previous value: -"One failed input ID and why it failed."New value: +"One failed input ID, why it failed, and what to do next."
changedOutput schema / properties / failed / items / properties / error / description
Previous value: -"What went wrong and how to resolve it."New value: +"What went wrong for this ID."
addedOutput schema / properties / failed / items / properties / reason
Added value: +{
+ "description": "Why this ID failed — a reason declared in this tool's error contract. Branch on it rather than on the message.",
+ "enum": [
+ "invalid_variant_id",
+ "variant_not_found",
+ "mitochondrial_unsupported",
+ "ambiguous_rsid",
+ "graphql_error",
+ "upstream_build_mismatch",
+ "upstream_unavailable",
+ "upstream_timeout",
+ "upstream_access",
+ "invalid_upstream_response"
+ ],
+ "type": "string"
+}
addedOutput schema / properties / failed / items / properties / recovery
Added value: +{
+ "description": "The next step for this ID — the recovery hint declared for its reason.",
+ "type": "string"
+}
changedOutput schema / properties / failed / items / required
Previous value: -[
- "variant",
- "error"
-]New value: +[
+ "variant",
+ "error",
+ "reason",
+ "recovery"
+]
addedOutput schema / properties / found / items / properties / in_silico / items / properties / annotation
Added value: +{
+ "description": "Text gnomAD attaches to the score — on gnomad_r3, the SpliceAI event (e.g. acceptor_gain, no_consequence). Holds the raw text when value is null for lack of a number; null for a plain score.",
+ "type": [
+ "string",
+ "null"
+ ]
+}
changedOutput schema / properties / found / items / properties / in_silico / items / properties / id / description
Previous value: -"Predictor name (e.g. revel_max, cadd, spliceai_ds_max)."New value: +"Predictor name. Ids vary by dataset — gnomad_r4: cadd, revel_max, spliceai_ds_max, pangolin_largest_ds, phylop, sift_max, polyphen_max; gnomad_r3: cadd, revel, splice_ai, primate_ai; gnomad_r2_1 and exac carry none."
changedOutput schema / properties / found / items / properties / in_silico / items / properties / value / description
Previous value: -"Predictor score; null when not provided for this variant."New value: +"Predictor score; null when not provided for this variant, or when gnomAD gave text with no number (the text is then in annotation)."
changedOutput schema / properties / found / items / properties / in_silico / items / required
Previous value: -[
- "id",
- "value"
-]New value: +[
+ "id",
+ "value",
+ "annotation"
+]