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  "Kind": "DirectoryIssues",
  "Slug": "gnomad-genetics-mcp-server",
  "Name": "gnomad-genetics-mcp-server",
  "CanonicalUrl": "https://askpod.ai/mcp/gnomad-genetics-mcp-server/issues",
  "ServerUrl": "https://askpod.ai/mcp/gnomad-genetics-mcp-server",
  "IssueTotal": 17,
  "Held": 16,
  "Issues": [
    {
      "Title": "bug(gnomad_get_variant): absent coordinate IDs fail as graphql_error instead of not-found",
      "Excerpt": "### Server version\n\n0.2.1\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0 / Node v26.5.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nAn absent coordinate variant surfaces as a generic GraphQL failure instead of as absence. For a missing variant, gnomAD returns HTTP 200 with one pathless error, `{\"message\":\"Variant not found\"}`, and `data: {\"variant\": null, \"clinvar_variant\": null}` on all four datasets. gnomAD strips `path` from every error it…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/25",
      "PublishedAt": "2026-08-31T03:48:59.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_get_variant): failed[] items drop the failure's reason and recovery hint",
      "Excerpt": "### Server version\n\n0.3.0\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\n`gnomad_get_variant` catches each item's service error and records only `err.message` in `failed[].error`. The error's `data.reason` and recovery hint are dropped, so a caller reading `failed[]` cannot branch on why an item failed or learn its next step. An item that exhausts retries reads `gnomAD is unavailable or rate-limited.` with no guidance,…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/43",
      "PublishedAt": "2026-09-30T09:44:26.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(chromosome-m): mitochondrial IDs, regions, and genes return false absence",
      "Excerpt": "### Server version\n\n0.3.0\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\ngnomAD serves mitochondrial variants through separate fields (`mitochondrial_variant`, `gene.mitochondrial_variants`, `mitochondrial_coverage`). The server accepts chromosome `M` in coordinate variant IDs and regions and resolves mitochondrial genes, but it queries only the nuclear fields, which answer with nothing. Callers get absence for variants…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/42",
      "PublishedAt": "2026-09-30T09:44:19.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_search_clinvar): query syntax in gene escapes the [gene] field",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\n`gnomad_search_clinvar` splices `gene` into the ESearch term as `${gene}[gene]` with no character check. A value carrying E-utilities query syntax (parentheses, brackets, quotes, a trailing `OR`/`AND`/`NOT`) detaches the `[gene]` tag, NCBI rewrites the term to `[All Fields]`, and the tool returns other genes' records labeled as the requested gene.…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/40",
      "PublishedAt": "2026-09-24T06:14:14.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(upstream-errors): gnomAD's caller-correctable 500 messages retry as upstream_unavailable",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\ngnomAD answers some caller-correctable requests with HTTP 500 and a user-facing GraphQL message. The server classifies every 5xx as `upstream_unavailable`, retries it four times, and drops the message. A region under the 2.5 Mb span limit that holds more than gnomAD's per-region ceiling of 30,000 variants is the case no local pre-check can predict…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/39",
      "PublishedAt": "2026-09-24T05:37:15.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(error-contracts): sanitizer reasons reach callers undeclared",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\nThe gnomAD and ClinVar services put a typed `data.reason` on every failure, but the tools' and resources' `errors[]` contracts declare few of them. Callers receive reasons no definition advertises, and every undeclared reason except the two the sanitizer hard-codes reaches the wire with no recovery hint. Undeclared today:\n\n| Surface | Reachable,…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/38",
      "PublishedAt": "2026-09-24T05:19:36.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(canvas): staging tools return ~120 KB per call — preview budget lands on both surfaces",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\nWith DataCanvas enabled, `gnomad_search_clinvar` and `gnomad_list_gene_variants` call `spillover()` with `previewChars: 60_000`, and the preview rows land on both surfaces — `structuredContent.preview` and the `format()` text. One call therefore returns roughly twice the preview budget, ~30k tokens, before the caller has asked for anything beyond…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/37",
      "PublishedAt": "2026-09-24T05:19:34.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_get_variant): gnomad_r3 SpliceAI values become NaN and fail every batch containing one",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\nOn `gnomad_r3`, gnomAD returns `splice_ai` as a score followed by the SpliceAI event in parentheses, e.g. `\"0.00 (no_consequence)\"`. `GnomadService` maps every predictor with `Number(p.value)`, so these values become `NaN`. `gnomad_get_variant` output validation then rejects the whole response, losing every variant in the batch, including those…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/36",
      "PublishedAt": "2026-09-24T04:55:04.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_get_coverage): positions counts gnomAD's coverage buckets, not bases",
      "Excerpt": "### Server version\n\n0.3.0\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\ngnomAD returns region, gene, and transcript coverage in buckets of `max(floor(span / 500), 1)` bp (`graphql-api/src/queries/coverage-queries.ts` in `broadinstitute/gnomad-browser`). `getCoverage()` reports `positions: bins.length`, which the output schema describes as \"Number of base positions summarized across the target\", so any target longer…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/45",
      "PublishedAt": "2026-09-30T09:44:40.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(canvas): fit-inline calls mint empty canvases and leave reused tables stale",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`gnomad_list_gene_variants` and `gnomad_search_clinvar` call `canvas.acquire(input.canvas_id, ctx)` before `spillover()` decides whether to stage anything. Two defects follow:\n\n- A call whose result fits inline, with no `canvas_id` supplied, still mints a new canvas that holds no table. Minted canvases count against…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/35",
      "PublishedAt": "2026-09-24T04:48:46.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_search_clinvar): format() claims the canvas is disabled when it is enabled",
      "Excerpt": "### Server version\n\n0.2.2\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nWith `CANVAS_PROVIDER_TYPE=duckdb` set, `gnomad_search_clinvar` given an Ensembl gene ID renders `**Canvas disabled** — inline preview only.`, which tells the model the SQL path is unavailable when it is available. The Ensembl-ID short-circuit returns `canvas_id: ''` without calling `canvas.acquire()`, and `format()` treats any…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/33",
      "PublishedAt": "2026-09-20T18:43:22.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_dataframe_query): bound results without cross-surface data loss",
      "Excerpt": "### Server version\n\n0.2.1\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0 / Node v26.5.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nRelated: #21, #37\n\n`gnomad_dataframe_query` puts every row the SQL produces into `structuredContent.rows`, up to the canvas row cap (`CANVAS_DEFAULT_ROW_LIMIT`, 10,000 by default), while `format()` renders the first 50 and then `… and N more row(s).` `content[]` readers cannot reach the rest, one call can return…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/30",
      "PublishedAt": "2026-08-31T03:49:21.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(region): unsupported chromosomes and out-of-range regions retry as upstream_unavailable",
      "Excerpt": "### Server version\n\n0.2.1\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0 / Node v26.5.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nRelated: #1, #39\n\ngnomAD rejects a region deterministically, with HTTP 500 and a GraphQL error message, on every dataset when it breaks any of these rules:\n\n- the chromosome is outside `1`–`22`, `X`, `Y`, `M` (exact case, no `chr` prefix, no `MT`, no zero-padding);\n- start is less than 1, or stop is 1,000,000,000 or…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/27",
      "PublishedAt": "2026-08-31T03:49:08.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(gnomad_get_gene_constraint): exac serves v2.1.1 metrics and no output names the constraint release",
      "Excerpt": "### Server version\n\n0.2.1\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0 / Node v26.5.0\n\n### Transport\n\nstdio\n\n### Description\n\n`gnomad_get_gene_constraint` sends gnomAD only the reference genome and echoes the requested `dataset` as provenance. `gene.gnomad_constraint` takes no arguments, so the build picks the table (gnomAD v4.1.2 on GRCh38, v2.1.1 on GRCh37). ExAC constraint lives in `gene.exac_constraint` (GRCh37), which the server never requests. So…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/26",
      "PublishedAt": "2026-08-31T03:49:04.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(docker): multi-arch image ships the builder's @duckdb binding, not the target platform's",
      "Excerpt": "Related: #7\n\n`Dockerfile:80` copies `node_modules/@duckdb` out of the build stage:\n\n```dockerfile\nCOPY --from=build /usr/src/app/node_modules/@duckdb ./node_modules/@duckdb\n```\n\nSince `Dockerfile:7` pins the build stage to `--platform=$BUILDPLATFORM`, that stage resolves dependencies for the **builder's** platform, not the target's. `@duckdb/node-bindings` declares one optionalDependency per platform and installs exactly one of them:\n\n```\n$ ls node_modules/@duckdb          # on an arm64 macOS…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/24",
      "PublishedAt": "2026-08-25T06:58:26.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(config): default MCP_SESSION_MODE to stateless across env, Docker, and src",
      "Excerpt": "`Dockerfile` sets `ENV MCP_SESSION_MODE=\"stateless\"`, but `.env.example` carries a commented `# MCP_SESSION_MODE=stateful`, whose comment documents the value set as `stateful | stateless (default: stateful)`. The container and the same code run via `bunx`, `npm start`, or from source therefore resolve to different session modes — stateless in Docker, stateful everywhere else, since the framework schema defaults to `auto` and `auto` resolves to `stateful`.\n\nThe hosted deployment runs stateless…",
      "SourceUrl": "https://github.com/cyanheads/gnomad-genetics-mcp-server/issues/23",
      "PublishedAt": "2026-08-22T19:00:44.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    }
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