gff-nostream 3.0.6 → 3.0.8

package/README.md

@@ -8,7 +8,7 @@ Parse GFF3 data. A simplified version of
 
 ## Install
 
-    $ npm install gff-nostream
+    $ pnpm add gff-nostream
 
 ## Usage
 
@@ -16,15 +16,25 @@ Parse GFF3 data. A simplified version of
 import { parseStringSync } from 'gff-nostream'
 import fs from 'fs'
 
-const stringOfGFF3 = fs.readFileSync('my_annotations.gff3', 'utf8')
-const features = parseStringSync(stringOfGFF3)
+const features = parseStringSync(fs.readFileSync('my_annotations.gff3', 'utf8'))
+```
+
+For browser or other non-Node environments, pass any GFF3 string directly — for
+example from `fetch`:
+
+```js
+import { parseStringSyncJBrowse } from 'gff-nostream'
+
+const text = await fetch('my_annotations.gff3').then(r => r.text())
+const features = parseStringSyncJBrowse(text)
 ```
 
 ## Object format
 
-In GFF3, features can have more than one location. Features are returned as
-arrays of all lines sharing the same ID. Values that are `.` in GFF3 are `null`
-in the output.
+### GFF3 format
+
+Features are returned as arrays of all lines sharing the same ID (to represent
+multi-location features). Values that are `.` in GFF3 are `null` in the output.
 
 A simple feature located in one place:
 
@@ -88,31 +98,68 @@ A CDS called `cds00001` located in two places:
 ]
 ```
 
+### JBrowse format
+
+The `JBrowse` variants return flat objects with coordinates converted to 0-based
+half-open, `strand` as a number (`1`/`-1`/`0`), attributes spread as lowercase
+top-level keys, and `subfeatures` instead of `child_features`.
+
+The same gene feature in JBrowse format:
+
+```json
+{
+  "refName": "ctg123",
+  "source": null,
+  "type": "gene",
+  "start": 999,
+  "end": 9000,
+  "strand": 1,
+  "subfeatures": [],
+  "id": "gene00001",
+  "name": "EDEN"
+}
+```
+
+Note: multi-location features (same ID on multiple lines) are not merged in
+JBrowse format — only the first occurrence is kept.
+
 ## API
 
 ### `parseStringSync(str: string): GFF3Feature[]`
 
-Synchronously parse a GFF3 string and return an array of features.
+Synchronously parse a GFF3 string and return an array of features. Comments,
+directives, and `##FASTA` sections are ignored.
 
 ### `parseStringSyncJBrowse(str: string): JBrowseFeature[]`
 
-Synchronously parse a GFF3 string and return features in JBrowse format (flat
-objects with `subfeatures` instead of `child_features`).
+Synchronously parse a GFF3 string and return features in JBrowse format.
 
 ### `parseRecords(records: LineRecord[]): GFF3Feature[]`
 
 Parse an array of `LineRecord` objects. Useful when managing raw line data
-directly (e.g. from an indexed file with byte offsets).
+directly (e.g. from a tabix-indexed file with byte offsets).
 
 ### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
 
 Same as `parseRecords` but returns JBrowse-format features.
 
+### `LineRecord`
+
+```ts
+interface LineRecord {
+  line: string
+  hasEscapes: boolean // set true when line contains '%' to enable URL-decoding
+  lineHash?: string | number // propagated to attributes._lineHash on the parsed feature
+  start?: number // byte offset passthrough (not used by the parser)
+  end?: number // byte offset passthrough (not used by the parser)
+}
+```
+
 ## Publishing
 
 [Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
 Actions.
 
 ```bash
-npm version patch  # or minor/major
+pnpm version patch  # or minor/major
 ```

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gff-nostream",
-  "version": "3.0.6",
+  "version": "3.0.8",
   "description": "utilities to read GFF3 data",
   "license": "MIT",
   "repository": {
@@ -48,13 +48,13 @@
   ],
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.6.2",
-    "eslint": "^10.3.0",
+    "@types/node": "^25.8.0",
+    "eslint": "^10.4.0",
     "eslint-plugin-import-x": "^4.16.2",
     "prettier": "^3.8.3",
     "rimraf": "^6.1.3",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.59.2",
-    "vitest": "^4.1.5"
+    "typescript-eslint": "^8.59.3",
+    "vitest": "^4.1.6"
   }
 }