msa-parsers 1.0.5 → 1.0.6

package/README.md

@@ -0,0 +1,89 @@
+# msa-parsers
+
+A TypeScript library for parsing multiple sequence alignment (MSA) files and
+related formats.
+
+Part of [react-msaview](../) (JBrowseMSA).
+
+## Installation
+
+```bash
+npm install msa-parsers
+# or
+yarn add msa-parsers
+```
+
+## Supported formats
+
+### MSA formats
+
+- **Stockholm** - Stockholm format (used by Pfam, Rfam)
+- **FASTA** - Aligned FASTA format
+- **Clustal** - ClustalW/ClustalX format
+- **A3M** - A3M format (used by HHsuite)
+- **EMF** - Ensembl Multi Format
+
+### Other formats
+
+- **Newick** - Phylogenetic tree format
+- **GFF** - General Feature Format (with InterProScan conversion utilities)
+
+## Usage
+
+### Parsing MSA files
+
+The `parseMSA` function auto-detects the format:
+
+```typescript
+import { parseMSA } from 'msa-parsers'
+
+const msa = parseMSA(fileContents)
+
+// Get sequence names
+const names = msa.getNames()
+
+// Get a specific row
+const sequence = msa.getRow('sequence_name')
+
+// Get alignment width
+const width = msa.getWidth()
+
+// Get phylogenetic tree (if available)
+const tree = msa.getTree()
+```
+
+### Using specific parsers
+
+```typescript
+import { FastaMSA, StockholmMSA, ClustalMSA } from 'msa-parsers'
+
+const fasta = new FastaMSA(fastaContents)
+const stockholm = new StockholmMSA(stockholmContents)
+const clustal = new ClustalMSA(clustalContents)
+```
+
+### Parsing Newick trees
+
+```typescript
+import { parseNewick, generateNodeIds } from 'msa-parsers'
+
+const tree = parseNewick('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);')
+const treeWithIds = generateNodeIds(tree)
+```
+
+### GFF and InterProScan utilities
+
+```typescript
+import { parseGFF, gffToInterProResults, interProToGFF } from 'msa-parsers'
+
+// Parse GFF file
+const records = parseGFF(gffContents)
+
+// Convert between GFF and InterProScan formats
+const interProResults = gffToInterProResults(records)
+const gffString = interProToGFF(interProResults, seqId)
+```
+
+## License
+
+MIT

package/dist/gff/gffToInterPro.d.ts

@@ -1,4 +1,4 @@
-import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../types';
+import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../types.ts';
 /**
  * Convert GFF records to InterProScan format
  *

package/dist/gff/index.d.ts

@@ -1,3 +1,3 @@
-export { parseGFF } from './parseGFF';
-export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
-export { interProResponseToGFF, interProToGFF } from './interProToGFF';
+export { parseGFF } from './parseGFF.ts';
+export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.ts';
+export { interProResponseToGFF, interProToGFF } from './interProToGFF.ts';

package/dist/gff/index.js

@@ -1,4 +1,4 @@
-export { parseGFF } from './parseGFF';
-export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
-export { interProResponseToGFF, interProToGFF } from './interProToGFF';
+export { parseGFF } from "./parseGFF.js";
+export { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
+export { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
 //# sourceMappingURL=index.js.map

package/dist/gff/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/gff/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAChF,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA"}

package/dist/gff/interProToGFF.d.ts

@@ -1,4 +1,4 @@
-import type { InterProScanResults } from '../types';
+import type { InterProScanResults } from '../types.ts';
 /**
  * Convert InterProScan results to GFF3 format
  */

package/dist/gff/parseGFF.d.ts

@@ -1,2 +1,2 @@
-import type { GFFRecord } from '../types';
+import type { GFFRecord } from '../types.ts';
 export declare function parseGFF(str?: string): GFFRecord[];

package/dist/index.d.ts

@@ -1,5 +1,5 @@
-export * from './types';
-export { generateNodeIds } from './util';
-export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa';
-export type { MSAParserType } from './msa';
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff';
+export * from './types.ts';
+export { generateNodeIds } from './util.ts';
+export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
+export type { MSAParserType } from './msa/index.ts';
+export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';

package/dist/index.js

@@ -1,9 +1,9 @@
 // Types
-export * from './types';
+export * from "./types.js";
 // Utilities
-export { generateNodeIds } from './util';
+export { generateNodeIds } from "./util.js";
 // MSA parsers
-export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa';
+export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from "./msa/index.js";
 // GFF parsing
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff';
+export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from "./gff/index.js";
 //# sourceMappingURL=index.js.map

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package/dist/msa/A3mMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types';
+import type { NodeWithIds } from '../types.ts';
 export default class A3mMSA {
     private MSA;
     private orderedNames;

package/dist/msa/ClustalMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types';
+import type { NodeWithIds } from '../types.ts';
 export default class ClustalMSA {
     private MSA;
     constructor(text: string);

package/dist/msa/EmfMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types';
+import type { NodeWithIds } from '../types.ts';
 export default class EmfMSA {
     private MSA;
     constructor(text: string);

package/dist/msa/FastaMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types';
+import type { NodeWithIds } from '../types.ts';
 export default class FastaMSA {
     private MSA;
     constructor(text: string);

package/dist/msa/StockholmMSA.d.ts

@@ -1,5 +1,5 @@
-import type { NodeWithIds } from '../types';
-import type { StockholmData } from './stockholmParser';
+import type { NodeWithIds } from '../types.ts';
+import type { StockholmData } from './stockholmParser.ts';
 export default class StockholmMSA {
     private data;
     private MSA;
@@ -51,4 +51,4 @@ export default class StockholmMSA {
         };
     })[];
 }
-export { sniff as stockholmSniff } from './stockholmParser';
+export { sniff as stockholmSniff } from './stockholmParser.ts';

package/dist/msa/StockholmMSA.js

@@ -1,6 +1,6 @@
-import parseNewick from './parseNewick';
-import { parseAll } from './stockholmParser';
-import { generateNodeIds } from '../util';
+import parseNewick from "./parseNewick.js";
+import { parseAll } from "./stockholmParser.js";
+import { generateNodeIds } from "../util.js";
 export default class StockholmMSA {
     data;
     MSA;
@@ -109,5 +109,5 @@ export default class StockholmMSA {
         ];
     }
 }
-export { sniff as stockholmSniff } from './stockholmParser';
+export { sniff as stockholmSniff } from "./stockholmParser.js";
 //# sourceMappingURL=StockholmMSA.js.map

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package/dist/msa/index.d.ts

@@ -1,18 +1,18 @@
-import A3mMSA from './A3mMSA';
-import ClustalMSA from './ClustalMSA';
-import EmfMSA from './EmfMSA';
-import FastaMSA from './FastaMSA';
-import StockholmMSA from './StockholmMSA';
+import A3mMSA from './A3mMSA.ts';
+import ClustalMSA from './ClustalMSA.ts';
+import EmfMSA from './EmfMSA.ts';
+import FastaMSA from './FastaMSA.ts';
+import StockholmMSA from './StockholmMSA.ts';
 export { parseEmfTree } from 'emf-js';
-export { default as parseNewick } from './parseNewick';
+export { default as parseNewick } from './parseNewick.ts';
 export type MSAParserType = StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA;
 export declare function parseMSA(text: string, currentAlignment?: number): MSAParserType;
 /**
  * Get ungapped sequence from an aligned row
  */
 export declare function getUngappedSequence(alignedSeq: string): string;
-export { default as A3mMSA } from './A3mMSA';
-export { default as ClustalMSA } from './ClustalMSA';
-export { default as EmfMSA } from './EmfMSA';
-export { default as FastaMSA } from './FastaMSA';
-export { default as StockholmMSA, stockholmSniff } from './StockholmMSA';
+export { default as A3mMSA } from './A3mMSA.ts';
+export { default as ClustalMSA } from './ClustalMSA.ts';
+export { default as EmfMSA } from './EmfMSA.ts';
+export { default as FastaMSA } from './FastaMSA.ts';
+export { default as StockholmMSA, stockholmSniff } from './StockholmMSA.ts';

package/dist/msa/index.js

@@ -1,10 +1,10 @@
-import A3mMSA from './A3mMSA';
-import ClustalMSA from './ClustalMSA';
-import EmfMSA from './EmfMSA';
-import FastaMSA from './FastaMSA';
-import StockholmMSA, { stockholmSniff } from './StockholmMSA';
+import A3mMSA from "./A3mMSA.js";
+import ClustalMSA from "./ClustalMSA.js";
+import EmfMSA from "./EmfMSA.js";
+import FastaMSA from "./FastaMSA.js";
+import StockholmMSA, { stockholmSniff } from "./StockholmMSA.js";
 export { parseEmfTree } from 'emf-js';
-export { default as parseNewick } from './parseNewick';
+export { default as parseNewick } from "./parseNewick.js";
 export function parseMSA(text, currentAlignment = 0) {
     if (stockholmSniff(text)) {
         return new StockholmMSA(text, currentAlignment);
@@ -26,9 +26,9 @@ export function parseMSA(text, currentAlignment = 0) {
 export function getUngappedSequence(alignedSeq) {
     return alignedSeq.replaceAll(/[.-]/g, '');
 }
-export { default as A3mMSA } from './A3mMSA';
-export { default as ClustalMSA } from './ClustalMSA';
-export { default as EmfMSA } from './EmfMSA';
-export { default as FastaMSA } from './FastaMSA';
-export { default as StockholmMSA, stockholmSniff } from './StockholmMSA';
+export { default as A3mMSA } from "./A3mMSA.js";
+export { default as ClustalMSA } from "./ClustalMSA.js";
+export { default as EmfMSA } from "./EmfMSA.js";
+export { default as FastaMSA } from "./FastaMSA.js";
+export { default as StockholmMSA, stockholmSniff } from "./StockholmMSA.js";
 //# sourceMappingURL=index.js.map

package/dist/msa/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAEhE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AASzD,MAAM,UAAU,QAAQ,CAAC,IAAY,EAAE,gBAAgB,GAAG,CAAC;IACzD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}

package/dist/util.d.ts

@@ -1,2 +1,2 @@
-import type { Node, NodeWithIds } from './types';
+import type { Node, NodeWithIds } from './types.ts';
 export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;

package/package.json

@@ -1,9 +1,14 @@
 {
   "name": "msa-parsers",
-  "version": "1.0.5",
+  "version": "1.0.6",
   "license": "MIT",
-  "main": "dist/index.js",
-  "module": "dist/index.js",
+  "type": "module",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "default": "./dist/index.js"
+    }
+  },
   "types": "dist/index.d.ts",
   "files": [
     "dist",
@@ -21,5 +26,9 @@
   },
   "publishConfig": {
     "access": "public"
+  },
+  "devDependencies": {
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.18"
   }
 }

package/src/gff/gffToInterPro.test.ts

@@ -1,8 +1,8 @@
 import { describe, expect, test } from 'vitest'
 
-import { gffToInterProResponse, gffToInterProResults } from './gffToInterPro'
+import { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.ts'
 
-import type { GFFRecord } from '../types'
+import type { GFFRecord } from '../types.ts'
 
 describe('gffToInterProResults', () => {
   test('converts empty array', () => {

package/src/gff/gffToInterPro.ts

@@ -2,7 +2,7 @@ import type {
   GFFRecord,
   InterProScanResponse,
   InterProScanResults,
-} from '../types'
+} from '../types.ts'
 
 /**
  * Convert GFF records to InterProScan format

package/src/gff/index.ts

@@ -1,3 +1,3 @@
-export { parseGFF } from './parseGFF'
-export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro'
-export { interProResponseToGFF, interProToGFF } from './interProToGFF'
+export { parseGFF } from './parseGFF.ts'
+export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.ts'
+export { interProResponseToGFF, interProToGFF } from './interProToGFF.ts'

package/src/gff/interProToGFF.test.ts

@@ -1,8 +1,8 @@
 import { describe, expect, test } from 'vitest'
 
-import { interProResponseToGFF, interProToGFF } from './interProToGFF'
+import { interProResponseToGFF, interProToGFF } from './interProToGFF.ts'
 
-import type { InterProScanResults } from '../types'
+import type { InterProScanResults } from '../types.ts'
 
 describe('interProToGFF', () => {
   test('converts empty results', () => {

package/src/gff/interProToGFF.ts

@@ -1,4 +1,4 @@
-import type { InterProScanResults } from '../types'
+import type { InterProScanResults } from '../types.ts'
 
 /**
  * Convert InterProScan results to GFF3 format

package/src/gff/parseGFF.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, test } from 'vitest'
 
-import { parseGFF } from './parseGFF'
+import { parseGFF } from './parseGFF.ts'
 
 describe('parseGFF', () => {
   test('parses empty string', () => {

package/src/gff/parseGFF.ts

@@ -1,4 +1,4 @@
-import type { GFFRecord } from '../types'
+import type { GFFRecord } from '../types.ts'
 
 function parseAttributes(col9?: string): Record<string, string | undefined> {
   if (!col9) {

package/src/index.ts

@@ -1,8 +1,8 @@
 // Types
-export * from './types'
+export * from './types.ts'
 
 // Utilities
-export { generateNodeIds } from './util'
+export { generateNodeIds } from './util.ts'
 
 // MSA parsers
 export {
@@ -16,8 +16,8 @@ export {
   parseMSA,
   parseNewick,
   stockholmSniff,
-} from './msa'
-export type { MSAParserType } from './msa'
+} from './msa/index.ts'
+export type { MSAParserType } from './msa/index.ts'
 
 // GFF parsing
 export {
@@ -26,4 +26,4 @@ export {
   interProResponseToGFF,
   interProToGFF,
   parseGFF,
-} from './gff'
+} from './gff/index.ts'

package/src/msa/A3mMSA.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, test } from 'vitest'
 
-import A3mMSA from './A3mMSA'
+import A3mMSA from './A3mMSA.ts'
 
 describe('A3mMSA', () => {
   describe('sniff', () => {

package/src/msa/A3mMSA.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types'
+import type { NodeWithIds } from '../types.ts'
 
 /**
  * A3M Format Parser

package/src/msa/ClustalMSA.ts

@@ -1,6 +1,6 @@
 import { parse } from 'clustal-js'
 
-import type { NodeWithIds } from '../types'
+import type { NodeWithIds } from '../types.ts'
 
 export default class ClustalMSA {
   private MSA: ReturnType<typeof parse>

package/src/msa/EmfMSA.ts

@@ -1,6 +1,6 @@
 import { parseEmfAln } from 'emf-js'
 
-import type { NodeWithIds } from '../types'
+import type { NodeWithIds } from '../types.ts'
 
 export default class EmfMSA {
   private MSA: ReturnType<typeof parseEmfAln>

package/src/msa/FastaMSA.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types'
+import type { NodeWithIds } from '../types.ts'
 
 export default class FastaMSA {
   private MSA: { seqdata: Record<string, string> }

package/src/msa/StockholmMSA.ts

@@ -1,9 +1,9 @@
-import parseNewick from './parseNewick'
-import { parseAll } from './stockholmParser'
-import { generateNodeIds } from '../util'
+import parseNewick from './parseNewick.ts'
+import { parseAll } from './stockholmParser.ts'
+import { generateNodeIds } from '../util.ts'
 
-import type { NodeWithIds } from '../types'
-import type { StockholmData } from './stockholmParser'
+import type { NodeWithIds } from '../types.ts'
+import type { StockholmData } from './stockholmParser.ts'
 
 export default class StockholmMSA {
   private data: StockholmData[]
@@ -138,4 +138,4 @@ export default class StockholmMSA {
   }
 }
 
-export { sniff as stockholmSniff } from './stockholmParser'
+export { sniff as stockholmSniff } from './stockholmParser.ts'

package/src/msa/index.test.ts

@@ -1,9 +1,9 @@
 import { describe, expect, test } from 'vitest'
 
-import A3mMSA from './A3mMSA'
-import ClustalMSA from './ClustalMSA'
-import FastaMSA from './FastaMSA'
-import { getUngappedSequence, parseMSA } from './index'
+import A3mMSA from './A3mMSA.ts'
+import ClustalMSA from './ClustalMSA.ts'
+import FastaMSA from './FastaMSA.ts'
+import { getUngappedSequence, parseMSA } from './index.ts'
 
 describe('parseMSA', () => {
   test('parses FASTA format', () => {

package/src/msa/index.ts

@@ -1,11 +1,11 @@
-import A3mMSA from './A3mMSA'
-import ClustalMSA from './ClustalMSA'
-import EmfMSA from './EmfMSA'
-import FastaMSA from './FastaMSA'
-import StockholmMSA, { stockholmSniff } from './StockholmMSA'
+import A3mMSA from './A3mMSA.ts'
+import ClustalMSA from './ClustalMSA.ts'
+import EmfMSA from './EmfMSA.ts'
+import FastaMSA from './FastaMSA.ts'
+import StockholmMSA, { stockholmSniff } from './StockholmMSA.ts'
 
 export { parseEmfTree } from 'emf-js'
-export { default as parseNewick } from './parseNewick'
+export { default as parseNewick } from './parseNewick.ts'
 
 export type MSAParserType =
   | StockholmMSA
@@ -37,8 +37,8 @@ export function getUngappedSequence(alignedSeq: string): string {
   return alignedSeq.replaceAll(/[.-]/g, '')
 }
 
-export { default as A3mMSA } from './A3mMSA'
-export { default as ClustalMSA } from './ClustalMSA'
-export { default as EmfMSA } from './EmfMSA'
-export { default as FastaMSA } from './FastaMSA'
-export { default as StockholmMSA, stockholmSniff } from './StockholmMSA'
+export { default as A3mMSA } from './A3mMSA.ts'
+export { default as ClustalMSA } from './ClustalMSA.ts'
+export { default as EmfMSA } from './EmfMSA.ts'
+export { default as FastaMSA } from './FastaMSA.ts'
+export { default as StockholmMSA, stockholmSniff } from './StockholmMSA.ts'

package/src/msa/stockholmParser.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, test } from 'vitest'
 
-import { parse, parseAll, sniff } from './stockholmParser'
+import { parse, parseAll, sniff } from './stockholmParser.ts'
 
 describe('stockholmParser', () => {
   describe('sniff', () => {

package/src/util.ts

@@ -1,4 +1,4 @@
-import type { Node, NodeWithIds } from './types'
+import type { Node, NodeWithIds } from './types.ts'
 
 export function generateNodeIds(
   tree: Node,

package/dist/gff/gffToInterPro.test.d.ts

@@ -1 +0,0 @@
-export {};