@cyanheads/ensembl-mcp-server 0.4.3 → 0.5.0

package/changelog/0.4.x/0.4.4.md

@@ -0,0 +1,27 @@
+---
+summary: "mcp-ts-core 0.13.6 adoption: an unrecognized or misspelled argument key now succeeds instead of failing, argument rejections carry a reason and recovery hint under Invalid params, and every declared tool error closes with a (reason ...) suffix"
+breaking: false
+security: false
+---
+
+# 0.4.4 — 2026-09-19
+
+## Changed
+
+- **Tool calls tolerate minor argument mismatches instead of rejecting them** — an unrecognized top-level key is dropped, a differently-cased spelling of a declared parameter (`dbName` for `dbname`, `maxTranscriptConsequences` for `max_transcript_consequences`) is rewritten onto the real key, and a JSON-stringified array is parsed and retried once. Advertised `inputSchema` is unchanged; only calls that previously failed now succeed.
+- **Argument rejections report `Invalid params` (`-32602`)** instead of the previous validation-error code, with `data.reason: "invalid_arguments"` and a synthesized `Recovery: …` hint derived from the offending field and the root schema.
+- **Every declared tool error closes with `(reason <reason>)`** — e.g. `not_found`, `invalid_notation` — on the `content[]` text. `structuredContent.error.data.reason` already carried the reason and is unchanged; resource errors are unaffected.
+- **A caller that disconnects mid-call is reported as a cancellation**, not an internal server error.
+- **`sessionMode: 'stateless'`** is declared directly in `src/index.ts`, matching the deployment default it was previously left to.
+- **Bun engines floor raised to `>=1.4.0`**, matching the framework requirement.
+- **Framework scripts, skills, agent protocol, and issue templates** sync to `@cyanheads/mcp-ts-core` 0.13.6 — the development skill tree moves from `skills/` to `framework-skills/` so a plugin install no longer surfaces it to the installing agent, `devcheck` gains a Worker typecheck step and a README version-badge check, and a CodeQL workflow is added.
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` `^0.12.3` → `^0.13.6`
+- `zod` `^4.4.3` → `^4.6.5`
+- `@biomejs/biome` `^2.5.9` → `^2.5.14`
+- `@types/node` `^26.2.0` → `^26.6.1`
+- `ignore` `^7.0.6` → `^7.0.9`
+- `tsc-alias` `^1.9.2` → `^1.9.5`
+- `vitest` `^4.1.11` → `^5.0.1`

package/changelog/0.5.x/0.5.0.md

@@ -0,0 +1,25 @@
+---
+summary: "ensembl_query_region caps its feature list (max_results) and returns assemblyName; ensembl_get_sequence returns bounded offset/max_length windows; oversized, reversed, and out-of-bounds regions classify as invalid_region; blank required identifiers are rejected at the schema across all tools"
+breaking: false
+security: false
+---
+
+# 0.5.0 — 2026-09-23
+
+## Changed
+
+- **`ensembl_get_sequence` returns bounded windows** — default 10,000 characters, with new `offset`/`max_length` params to page through the rest; `truncated`/`nextOffset` say how to continue, `length` stays the full sequence length ([#19](https://github.com/cyanheads/ensembl-mcp-server/issues/19)).
+- **`ensembl_query_region` caps its feature list** — `max_results` defaults to 100 (`0` for uncapped); `totalCount` always reports the true pre-cap count ([#17](https://github.com/cyanheads/ensembl-mcp-server/issues/17)).
+- **`ensembl_query_region` returns `assemblyName`** — read from the overlap rows or resolved via `/info/assembly` and cached per species for the process ([#23](https://github.com/cyanheads/ensembl-mcp-server/issues/23)).
+
+## Fixed
+
+- **`ensembl_query_region` rejects an empty `feature` array** at the schema instead of forwarding it to Ensembl ([#21](https://github.com/cyanheads/ensembl-mcp-server/issues/21)).
+- **Oversized, reversed, or out-of-bounds regions classify as `invalid_region`** on both region tools, with actionable recovery guidance — also undecodable regions on `ensembl_query_region` (limit 5,000,000 bases) and unknown sequence regions on `ensembl_get_sequence` (limit 10,000,000 bases), which rejects reversed coordinates before any request ([#24](https://github.com/cyanheads/ensembl-mcp-server/issues/24), [#27](https://github.com/cyanheads/ensembl-mcp-server/issues/27), [#28](https://github.com/cyanheads/ensembl-mcp-server/issues/28)).
+- **Both region tools classify Ensembl's error text in linear time** — the patterns matched against the echoed id or region no longer backtrack, and on `ensembl_get_sequence` an unknown stable ID whose echo reads like a type mismatch now reports `not_found` ([#27](https://github.com/cyanheads/ensembl-mcp-server/issues/27), [#28](https://github.com/cyanheads/ensembl-mcp-server/issues/28)).
+- **`ensembl_get_sequence` rejects a non-genomic `type` for a region id** as `type_mismatch` — `/sequence/region` ignores `type` and always serves genomic DNA, so the tool now fails the request instead of mislabeling it ([#25](https://github.com/cyanheads/ensembl-mcp-server/issues/25)).
+- **Blank or whitespace-only required identifiers are rejected at the schema** — `id`, `region`, `species`, `variant`, and batch `ids`/`symbols` entries across every tool, instead of reaching Ensembl unfiltered ([#22](https://github.com/cyanheads/ensembl-mcp-server/issues/22)).
+
+## Dependencies
+
+- `@types/node` `^26.6.1` → `^26.6.2`

package/changelog/template.md

@@ -6,8 +6,8 @@
 
 # Required. One-line GitHub Release-style headline. 350 character cap — a
 # ceiling, not a target. Default short and scannable. Don't pad, don't stitch
-# unrelated changes with commas/semicolons into an inventory — pick the
-# headline, like a tag's theme line. Quotes required: unquoted YAML treats
+# unrelated changes with commas/semicolons into an inventory — pick the one
+# headline the release is about. Quotes required: unquoted YAML treats
 # `: ` inside the value as a key separator and fails GitHub's strict parser.
 summary: ""
 
@@ -117,30 +117,13 @@ security: false
   in that unrelated item's metadata.
 
   TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
-  via `gh release create --notes-from-tag`. The tag is a derivative of this
-  changelog entry — a condensed, scannable version, not a copy. Format:
-
-    <theme — omit version number, GitHub prepends it>
-                                                          ← blank line
-    <1-2 sentence context: what this release does>
-                                                          ← blank line
-    Dependency bumps:                                     ← section header
-                                                          ← blank line
-    - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6          ← bullet
-                                                          ← blank line
-    Changed:                                              ← only sections with entries
-                                                          ← blank line
-    - `format()` output includes `query` in text mode
-                                                          ← blank line
-    Added:
-                                                          ← blank line
-    - `manifest.json` scaffolded for MCPB bundle support
-    - Install badges (Claude Desktop, Cursor, VS Code)
-                                                          ← blank line
-    <N> tests pass; `bun run devcheck` clean.             ← footer
-
-  Never a flat comma-separated string. Always structured markdown with
-  sections. The tag must scan well as a rendered GitHub Release page.
+  via `gh release create --notes-from-tag`. It is a condensed digest of this
+  entry, never a copy, and its format is owned by the `release-and-publish`
+  skill (step 4, "Create the annotated tag"): a short subject line without the
+  version, flat headline bullets — no Keep-a-Changelog section headers, no
+  gates line — at most one deps line, issue backlinks, and the changelog link
+  last. In release-PR mode the `git-wrapup` skill authors those bullets as the
+  PR body's `## Changes` and the tag copies them.
 -->
 
 ## Added

package/dist/index.js

@@ -19,6 +19,13 @@ import { initEnsemblService } from './services/ensembl/ensembl-service.js';
 await createApp({
     name: 'ensembl-mcp-server',
     title: 'ensembl-mcp-server',
+    /**
+     * Every tool here is a read-only Ensembl REST lookup — no handler calls
+     * `ctx.requestInput`, so nothing needs a session to come back to. `stateless`
+     * is declared in source rather than left to the deployment's
+     * `MCP_SESSION_MODE`, which still wins when it carries a meaningful value.
+     */
+    sessionMode: 'stateless',
     cacheHints: {
         'prompts/list': { ttlMs: 3_600_000, cacheScope: 'public' },
         'resources/list': { ttlMs: 3_600_000, cacheScope: 'public' },

package/dist/index.js.map

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package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.d.ts.map

@@ -1 +1 @@
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package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js

@@ -30,12 +30,18 @@ export const ensemblGeneDossierPrompt = prompt('ensembl_gene_dossier', {
                     `Record the stable ID (ENSG…), genomic coordinates (chr:start-end:strand:assembly), ` +
                     `biotype, and the canonical transcript ID (ENST…).\n\n` +
                     `2. **Fetch the protein sequence** — call \`ensembl_get_sequence\` with the canonical ` +
-                    `transcript ID from step 1 and type="protein". Record the amino acid sequence and its length.\n\n` +
+                    `transcript ID from step 1 and type="protein". Record the amino acid sequence and its length. ` +
+                    `A protein longer than 10,000 residues comes back as a first window (truncated=true); length ` +
+                    `is still the full length, and the window already holds the leading residues step 7 needs.\n\n` +
                     `3. **Find variants in the locus** — call \`ensembl_query_region\` with ` +
                     `species="${args.species}", the gene's chromosomal region (chr:start-end from step 1), ` +
-                    `and feature=["variation"]. Record the variant IDs (rsIDs), positions, consequence type, ` +
-                    `and any clinical significance. Functional impact (HIGH/MODERATE/LOW) is not reported by ` +
-                    `this step — it comes from VEP in step 4.\n\n` +
+                    `and feature=["variation"]. A gene locus can hold tens of thousands of variants, so the ` +
+                    `response returns the first 100 (max_results) while totalCount reports the full count — ` +
+                    `record totalCount as the locus variant count. To see other variants, query a narrower ` +
+                    `window (e.g. one exon's coordinates) or raise max_results. Record the variant IDs (rsIDs), ` +
+                    `positions, consequence type, and any clinical significance of the returned variants. ` +
+                    `Functional impact (HIGH/MODERATE/LOW) is not reported by this step — it comes from VEP ` +
+                    `in step 4.\n\n` +
                     `4. **Predict variant consequences** — for up to 3 variants from step 3, ` +
                     `call \`ensembl_predict_variant\` with each variant's rsID (e.g. rs334), HGVS notation, ` +
                     `or region+allele. This step returns the functional impact. ` +
@@ -50,7 +56,8 @@ export const ensemblGeneDossierPrompt = prompt('ensembl_gene_dossier', {
                     `7. **Synthesize the dossier** — compile your findings into a structured report with sections:\n` +
                     `   - Gene overview (ID, location, biotype, description)\n` +
                     `   - Protein sequence summary (length, first 50 aa, key domains if known)\n` +
-                    `   - Variant landscape (count, highest-impact findings, clinical significance)\n` +
+                    `   - Variant landscape (count from step 3's totalCount, highest-impact findings, ` +
+                    `clinical significance)\n` +
                     `   - Conservation across species (ortholog table with perc_id)\n` +
                     `   - External IDs for follow-up (UniProt → pubchem for structure, ` +
                     `HGNC/EntrezGene → pubmed for literature, OMIM for disease associations)\n\n` +

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package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkP7B,CAAC"}
+{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoP7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-homology.tool.js

@@ -57,6 +57,8 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
             'Cannot be combined with symbol.'),
         species: z
             .string()
+            .trim()
+            .min(1)
             .default('homo_sapiens')
             .describe('Source species (the species the query gene belongs to) in Ensembl internal format. ' +
             'Default is homo_sapiens. Use ensembl_list_species to discover valid values.'),

package/dist/mcp-server/tools/definitions/get-homology.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts

@@ -15,11 +15,16 @@ export declare const ensemblGetSequence: import("@cyanheads/mcp-ts-core").ToolDe
     species: z.ZodOptional<z.ZodString>;
     expand_5prime: z.ZodDefault<z.ZodNumber>;
     expand_3prime: z.ZodDefault<z.ZodNumber>;
+    offset: z.ZodDefault<z.ZodNumber>;
+    max_length: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     id: z.ZodString;
     type: z.ZodString;
     seq: z.ZodString;
     length: z.ZodNumber;
+    offset: z.ZodNumber;
+    truncated: z.ZodBoolean;
+    nextOffset: z.ZodOptional<z.ZodNumber>;
     description: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, readonly [{
     readonly reason: "not_found";
@@ -29,12 +34,19 @@ export declare const ensemblGetSequence: import("@cyanheads/mcp-ts-core").ToolDe
 }, {
     readonly reason: "type_mismatch";
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The requested sequence type is incompatible with the provided ID type.";
+    readonly when: "A non-genomic type (cdna, cds, or protein) was requested for a region id or a gene ID.";
     readonly recovery: string;
 }, {
     readonly reason: "missing_species";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "A bare chr:start-end region was given without a species.";
     readonly recovery: string;
-}], undefined>;
+}, {
+    readonly reason: "invalid_region";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: string;
+    readonly recovery: string;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=get-sequence.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgU7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-sequence.tool.js

@@ -6,24 +6,44 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getEnsemblService } from '../../../services/ensembl/ensembl-service.js';
 const SEQUENCE_TYPES = ['genomic', 'cdna', 'cds', 'protein'];
+/**
+ * Linear-time `/first.*second/i`: `first`, then `second` later on the same line.
+ * Ensembl echoes the caller's ID into its error text, and the backtracking regex
+ * is quadratic in that echo.
+ */
+function mentionsInOrder(msg, first, second) {
+    return msg
+        .toLowerCase()
+        .split(/[\n\r\u2028\u2029]/)
+        .some((line) => {
+        const at = line.indexOf(first);
+        return at !== -1 && line.includes(second, at + first.length);
+    });
+}
 export const ensemblGetSequence = tool('ensembl_get_sequence', {
     title: 'Get Sequence',
     description: 'Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. ' +
-        'Returns the sequence with its stable ID, molecule type, and character count — large sequences are ' +
-        'returned in full but the length is stated so callers can budget context. The type parameter selects ' +
-        'which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), ' +
-        'cds (coding sequence only), protein. For region mode, set id to a region — either ' +
-        'species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with ' +
-        'species set (e.g. id 13:32315086-32400268, species homo_sapiens). Protein sequences require a transcript or ' +
-        'protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene with expand_transcripts=true ' +
-        'to get the canonical transcript ID first.',
+        'Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, ' +
+        'molecule type, and full length. When more follows the window, truncated is true and nextOffset is the ' +
+        'offset to request next; walking nextOffset reconstructs the whole sequence, and max_length 0 returns ' +
+        'everything from offset to the end. The type parameter selects which sequence is fetched: genomic ' +
+        '(default, includes introns), cdna (spliced transcript), cds (coding sequence only), protein. ' +
+        'For region mode, set id to a region — either species:chr:start-end ' +
+        '(e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with species set ' +
+        '(e.g. id 13:32315086-32400268, species homo_sapiens), spanning at most 10,000,000 bases; ' +
+        'regions return genomic DNA only. Protein sequences require a transcript or protein stable ID ' +
+        '(ENST…/ENSP…), not a gene ID — use ' +
+        'ensembl_lookup_gene with expand_transcripts=true to get the canonical transcript ID first.',
     annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
     input: z.object({
         id: z
             .string()
+            .trim()
+            .min(1)
             .describe('Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. ' +
             'Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare ' +
-            'chr:start-end (e.g. 13:32315086-32400268) when the species field is set.'),
+            'chr:start-end (e.g. 13:32315086-32400268) when the species field is set. A region needs ' +
+            'start at or below end, within the sequence region, and spans at most 10,000,000 bases.'),
         type: z
             .enum(SEQUENCE_TYPES)
             .default('genomic')
@@ -31,7 +51,8 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             'genomic: full genomic DNA including introns (default). ' +
             'cdna: spliced transcript sequence (requires ENST… ID). ' +
             'cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). ' +
-            'protein: amino acid sequence (requires ENST… or ENSP… ID).'),
+            'protein: amino acid sequence (requires ENST… or ENSP… ID). ' +
+            'Region ids are genomic-only — request cdna, cds, or protein from a transcript or protein stable ID.'),
         species: z
             .string()
             .optional()
@@ -53,21 +74,52 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             .default(0)
             .describe("Number of base pairs to extend downstream (3' direction) of the requested feature. " +
             'Default 0. Only applies to genomic sequences and region queries.'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('0-based character offset where the returned window starts, counted in the resolved sequence ' +
+            '(including any expand_5prime/expand_3prime flank). Default 0. Pass nextOffset from a truncated ' +
+            'response to fetch the following window; an offset at or past the end returns an empty window.'),
+        max_length: z
+            .number()
+            .int()
+            .min(0)
+            .default(10_000)
+            .describe('Maximum number of characters in the returned window. Default 10000. ' +
+            'Set to 0 to return everything from offset to the end, uncapped.'),
     }),
     output: z.object({
         id: z.string().describe('The stable ID or region used for the lookup.'),
         type: z.string().describe('Sequence type returned (genomic, cdna, cds, or protein).'),
         seq: z
             .string()
-            .describe('The full sequence. DNA sequences use IUPAC nucleotide codes (ACGT + ambiguity codes). ' +
-            'Protein sequences use single-letter amino acid codes. ' +
-            'Large genomic sequences (e.g. 85 kb for BRCA2) are returned in full.'),
+            .describe('The requested window of the sequence: at most max_length characters starting at offset. ' +
+            'DNA sequences use IUPAC nucleotide codes (ACGT + ambiguity codes); protein sequences use ' +
+            'single-letter amino acid codes. Empty when offset is at or past the end.'),
         length: z
             .number()
-            .describe('Sequence length in characters — nucleotides for genomic/cdna/cds, amino-acid residues for protein. ' +
-            'Use this to budget context window usage before processing the sequence.'),
+            .describe('Full sequence length in characters, not the window size — nucleotides for genomic/cdna/cds, ' +
+            'amino-acid residues for protein. Includes any expand_5prime/expand_3prime flank.'),
+        offset: z.number().describe('0-based character offset where this window starts.'),
+        truncated: z
+            .boolean()
+            .describe('True when more sequence follows this window; request nextOffset to continue.'),
+        nextOffset: z
+            .number()
+            .optional()
+            .describe('Offset of the first character after this window — pass it as offset to fetch the next ' +
+            'window. Present only when truncated.'),
         description: z.string().optional().describe('Sequence description from Ensembl, if provided.'),
     }),
+    enrichment: {
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance about the window: how to continue when truncated, or why it is empty when the ' +
+            'offset is past the end.'),
+    },
     errors: [
         {
             reason: 'not_found',
@@ -79,10 +131,11 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
         {
             reason: 'type_mismatch',
             code: JsonRpcErrorCode.ValidationError,
-            when: 'The requested sequence type is incompatible with the provided ID type.',
-            recovery: 'protein and cds sequences require a transcript ID (ENST…) or protein ID (ENSP…), not a gene ID. ' +
+            when: 'A non-genomic type (cdna, cds, or protein) was requested for a region id or a gene ID.',
+            recovery: 'Region ids are genomic-only, and a gene ID serves only its genomic sequence. Request cdna or ' +
+                'cds from a transcript ID (ENST…) and protein from a transcript or protein ID (ENST…/ENSP…). ' +
                 'Use ensembl_lookup_gene with expand_transcripts=true to find the canonical transcript ID, ' +
-                'then request the protein or cds sequence from that transcript ID.',
+                'then request the sequence from that transcript ID.',
         },
         {
             reason: 'missing_species',
@@ -91,9 +144,24 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             recovery: 'Set species (e.g. homo_sapiens) alongside the chr:start-end region, ' +
                 'or use the combined species:chr:start-end id form.',
         },
+        {
+            reason: 'invalid_region',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'A region id has its start after its end, starts past the end of its sequence region, ' +
+                'spans more than the 10,000,000-base maximum, or names a sequence region the species lacks.',
+            recovery: 'Give start at or below end, within the sequence region length for the target assembly, ' +
+                'spanning at most 10,000,000 bases; split a longer region into windows of at most ' +
+                '10,000,000 bases. Name the chromosome as Ensembl does (13, X, MT; chr13 is also ' +
+                'accepted) — ensembl_lookup_gene reports valid coordinates for any gene.',
+        },
     ],
     async handler(input, ctx) {
-        ctx.log.info('Fetching sequence', { id: input.id, type: input.type });
+        ctx.log.info('Fetching sequence', {
+            id: input.id,
+            type: input.type,
+            offset: input.offset,
+            maxLength: input.max_length,
+        });
         const service = getEnsemblService();
         // Region mode accepts two id shapes:
         //   species:chr:start-end   embedded species (e.g. homo_sapiens:13:32315086-32400268)
@@ -104,7 +172,13 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
         // colon) matches neither, routing to stable-ID mode below.
         const isPrefixedRegion = /^[a-z_]+:[\w.]+:\d+-\d+$/i.test(input.id);
         const isBareRegion = /^[\w.]+:\d+-\d+$/.test(input.id);
+        let resolved;
         if (isPrefixedRegion || isBareRegion) {
+            // Ensembl's region endpoint serves genomic DNA only and ignores a type parameter,
+            // so a cdna/cds/protein request would come back as genomic — reject it up front.
+            if (input.type !== 'genomic') {
+                throw ctx.fail('type_mismatch', `Region ids are genomic-only — type "${input.type}" is not available for region ${input.id}.`, { ...ctx.recoveryFor('type_mismatch') });
+            }
             // For the prefixed form the species is the segment before the first colon and
             // the region is everything after it; the bare form takes its species from the
             // species field and uses the whole id as the region.
@@ -114,10 +188,25 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             if (!species) {
                 throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form.`, { ...ctx.recoveryFor('missing_species') });
             }
-            const seq = await service
+            // Both region shapes end in start-end after the last colon. Comparing the digit
+            // strings (length, then lexically) stays exact past double precision and linear
+            // in the caller's input, where BigInt parsing is not.
+            const [start = '', end = ''] = region
+                .slice(region.lastIndexOf(':') + 1)
+                .split('-')
+                .map((digits) => digits.replace(/^0+(?=\d)/, ''));
+            if (start.length > end.length || (start.length === end.length && start > end)) {
+                throw ctx.fail('invalid_region', `Region ${input.id} is reversed: start ${start} is greater than its end ${end}.`, { ...ctx.recoveryFor('invalid_region') });
+            }
+            resolved = await service
                 .getSequenceByRegion(species, region, input.expand_5prime, input.expand_3prime, ctx)
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
+                if (/cannot request a slice|maximum allowed length|no slice found/i.test(msg)) {
+                    throw ctx.fail('invalid_region', `Invalid region ${input.id}: ${msg}`, {
+                        ...ctx.recoveryFor('invalid_region'),
+                    });
+                }
                 if (/not found|invalid|no stable id/i.test(msg)) {
                     throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}`, {
                         ...ctx.recoveryFor('not_found'),
@@ -125,27 +214,54 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
                 }
                 throw err;
             });
-            return seq;
         }
-        // Stable ID mode
-        const seq = await service
-            .getSequenceById(input.id.trim(), input.type, input.expand_5prime, input.expand_3prime, ctx)
-            .catch((err) => {
-            const msg = err instanceof Error ? err.message : String(err);
-            if (/protein.*gene|cds.*gene|type.*mismatch|incompatible/i.test(msg) ||
-                /requesting a gene and type not equal/i.test(msg) ||
-                /multiple sequences detected/i.test(msg)) {
-                throw ctx.fail('type_mismatch', `Cannot request type "${input.type}" from a gene ID — use a transcript or protein stable ID instead. ` +
-                    `Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`, { ...ctx.recoveryFor('type_mismatch') });
-            }
-            if (/not found|no stable id/i.test(msg)) {
-                throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`, {
-                    ...ctx.recoveryFor('not_found'),
-                });
-            }
-            throw err;
-        });
-        return seq;
+        else {
+            resolved = await service
+                .getSequenceById(input.id, input.type, input.expand_5prime, input.expand_3prime, ctx)
+                .catch((err) => {
+                const msg = err instanceof Error ? err.message : String(err);
+                // Ensembl echoes the requested ID into "ID '<id>' not found", and the echo can
+                // contain any word — so the looser type heuristics never override a not-found.
+                const notFound = /not found|no stable id/i.test(msg);
+                if (/requesting a gene and type not equal|multiple sequences detected/i.test(msg) ||
+                    (!notFound &&
+                        (mentionsInOrder(msg, 'protein', 'gene') ||
+                            mentionsInOrder(msg, 'cds', 'gene') ||
+                            mentionsInOrder(msg, 'type', 'mismatch') ||
+                            /incompatible/i.test(msg)))) {
+                    throw ctx.fail('type_mismatch', `Cannot request type "${input.type}" from a gene ID — use a transcript or protein stable ID instead. ` +
+                        `Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`, { ...ctx.recoveryFor('type_mismatch') });
+                }
+                if (notFound) {
+                    throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
+                }
+                throw err;
+            });
+        }
+        // The window is a post-fetch slice of the resolved sequence, so it indexes past any
+        // expansion flank and `length` stays the full length. Ensembl's own start/end trim
+        // would hide the full length and cannot be combined with expansion.
+        const { length } = resolved;
+        const end = input.max_length > 0 ? Math.min(input.offset + input.max_length, length) : length;
+        const truncated = end < length;
+        if (input.offset >= length) {
+            ctx.enrich.notice(`No characters returned: offset ${input.offset} is at or past the end of the sequence, ` +
+                `which is ${length.toLocaleString()} characters long. Request an offset below the length.`);
+        }
+        else if (truncated) {
+            ctx.enrich.notice(`Showing ${(end - input.offset).toLocaleString()} of ${length.toLocaleString()} characters ` +
+                `from offset ${input.offset}. Call again with offset ${end} for the next window, or set ` +
+                'max_length to 0 for everything from offset to the end.');
+        }
+        return {
+            ...resolved,
+            seq: resolved.seq.slice(input.offset, end),
+            offset: input.offset,
+            truncated,
+            ...(truncated && { nextOffset: end }),
+        };
     },
     format: (result) => {
         const lines = [];
@@ -154,18 +270,17 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
         lines.push(`**Type:** ${result.type} | **Length:** ${result.length.toLocaleString()} ${unit}`);
         if (result.description)
             lines.push(`**Description:** ${result.description}`);
+        const extent = result.truncated
+            ? `truncated; next offset ${result.nextOffset}`
+            : 'not truncated (nothing follows this window)';
+        lines.push(`**Window:** ${result.seq.length.toLocaleString()} characters from offset ${result.offset} ` +
+            `of ${result.length.toLocaleString()} — ${extent}`);
         lines.push('');
-        // Show first 200 chars + truncation note for large sequences
-        if (result.seq.length > 200) {
-            lines.push('```');
-            lines.push(result.seq.slice(0, 200));
-            lines.push(`… (${result.length.toLocaleString()} total characters)`);
-            lines.push('```');
+        if (result.seq) {
+            lines.push('```', result.seq, '```');
         }
         else {
-            lines.push('```');
-            lines.push(result.seq);
-            lines.push('```');
+            lines.push('_No sequence characters at this offset._');
         }
         return [{ type: 'text', text: lines.join('\n') }];
     },