gff-nostream 3.0.4 → 3.0.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. package/README.md +8 -0
  2. package/dist/api.js +1 -1
  3. package/dist/api.js.map +1 -1
  4. package/dist/util.js +4 -4
  5. package/dist/util.js.map +1 -1
  6. package/esm/api.js.map +1 -1
  7. package/esm/util.js +4 -4
  8. package/esm/util.js.map +1 -1
  9. package/package.json +16 -13
  10. package/src/api.ts +1 -1
  11. package/src/util.ts +28 -28
package/README.md CHANGED
@@ -102,3 +102,11 @@ Parse an array of `LineRecord` objects. Useful when managing raw line data direc
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  ### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
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  Same as `parseRecords` but returns JBrowse-format features.
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+
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+ ## Publishing
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+
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+ [Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
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+
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+ ```bash
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+ npm version patch # or minor/major
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+ ```
package/dist/api.js CHANGED
@@ -64,7 +64,7 @@ function parseRecords(records) {
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  featureLine.child_features = [];
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  featureLine.derived_features = [];
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  if (record.lineHash !== undefined) {
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- featureLine.attributes ?? (featureLine.attributes = {});
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+ featureLine.attributes ??= {};
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  featureLine.attributes._lineHash = [String(record.lineHash)];
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  }
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  const attrs = featureLine.attributes;
package/dist/api.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/util.js CHANGED
@@ -233,16 +233,16 @@ function parseDirective(line) {
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  return {
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  ...parsed,
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  seq_id: c[0],
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- start: c[1]?.replaceAll(nonDigitRegex, ''),
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- end: c[2]?.replaceAll(nonDigitRegex, ''),
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+ start: c[1].replaceAll(nonDigitRegex, ''),
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+ end: c[2].replaceAll(nonDigitRegex, ''),
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  };
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  }
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  else if (name === 'genome-build') {
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  const [source, buildName] = contents.split(whitespaceRegex, 2);
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  return {
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  ...parsed,
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- source,
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- buildName,
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+ source: source,
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+ buildName: buildName,
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  };
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  }
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  return parsed;
package/dist/util.js.map CHANGED
@@ -1 +1 @@
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package/esm/api.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/util.js CHANGED
@@ -219,16 +219,16 @@ export function parseDirective(line) {
219
219
  return {
220
220
  ...parsed,
221
221
  seq_id: c[0],
222
- start: c[1]?.replaceAll(nonDigitRegex, ''),
223
- end: c[2]?.replaceAll(nonDigitRegex, ''),
222
+ start: c[1].replaceAll(nonDigitRegex, ''),
223
+ end: c[2].replaceAll(nonDigitRegex, ''),
224
224
  };
225
225
  }
226
226
  else if (name === 'genome-build') {
227
227
  const [source, buildName] = contents.split(whitespaceRegex, 2);
228
228
  return {
229
229
  ...parsed,
230
- source,
231
- buildName,
230
+ source: source,
231
+ buildName: buildName,
232
232
  };
233
233
  }
234
234
  return parsed;
package/esm/util.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "gff-nostream",
3
- "version": "3.0.4",
3
+ "version": "3.0.5",
4
4
  "description": "utilities to read GFF3 data",
5
5
  "license": "MIT",
6
6
  "repository": {
@@ -8,7 +8,7 @@
8
8
  "url": "https://github.com/GMOD/gff-nostream.git"
9
9
  },
10
10
  "type": "module",
11
- "types": "./dist/index.d.ts",
11
+ "main": "dist/index.js",
12
12
  "exports": {
13
13
  "import": "./esm/index.js",
14
14
  "require": "./dist/index.js"
@@ -25,18 +25,19 @@
25
25
  ],
26
26
  "scripts": {
27
27
  "test": "vitest",
28
- "benchonly": "vitest bench",
29
- "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
30
- "clean": "rm -rf dist esm",
31
- "lint": "eslint --report-unused-disable-directives --max-warnings 0",
28
+ "clean": "rimraf dist esm",
32
29
  "format": "prettier --write .",
33
- "prebuild": "yarn clean",
34
- "build:esm": "tsc --target esnext --outDir esm",
35
- "build:es5": "tsc --target es2020 --module commonjs --moduleResolution bundler --outDir dist",
30
+ "lint": "eslint --report-unused-disable-directives --max-warnings 0",
31
+ "prebuild": "pnpm clean",
32
+ "build:esm": "tsc --outDir esm",
33
+ "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
36
34
  "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
37
- "build": "yarn build:es5 && yarn build:esm",
38
- "prepublishOnly": "yarn test --run && yarn build",
39
- "postversion": "git push --follow-tags"
35
+ "preversion": "pnpm lint && pnpm test --run && pnpm build",
36
+ "postversion": "git push --follow-tags",
37
+ "build": "pnpm build:esm && pnpm build:es5",
38
+ "benchonly": "vitest bench",
39
+ "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
40
+ "prepublishOnly": "pnpm test --run && pnpm build"
40
41
  },
41
42
  "keywords": [
42
43
  "bionode",
@@ -46,10 +47,12 @@
46
47
  "genomics"
47
48
  ],
48
49
  "devDependencies": {
50
+ "@eslint/js": "^10.0.1",
49
51
  "@types/node": "^25.6.0",
50
52
  "eslint": "^10.2.1",
51
- "eslint-plugin-import": "^2.32.0",
53
+ "eslint-plugin-import-x": "^4.16.2",
52
54
  "prettier": "^3.8.3",
55
+ "rimraf": "^6.1.3",
53
56
  "typescript": "^6.0.3",
54
57
  "typescript-eslint": "^8.59.0",
55
58
  "vitest": "^4.1.5"
package/src/api.ts CHANGED
@@ -100,7 +100,7 @@ export function parseRecords(records: LineRecord[]): GFF3Feature[] {
100
100
 
101
101
  let feature: GFF3Feature
102
102
  if (ids) {
103
- const id = ids[0]
103
+ const id = ids[0]!
104
104
  const existing = byId.get(id)
105
105
  if (existing) {
106
106
  existing.push(featureLine)
package/src/util.ts CHANGED
@@ -135,17 +135,17 @@ function parseFeatureImpl(
135
135
  shouldUnescape: boolean,
136
136
  ): GFF3FeatureLine {
137
137
  const f = line.split('\t')
138
- const startStr = f[3]
139
- const endStr = f[4]
140
- const scoreStr = f[5]
141
- const strand = f[6]
142
- const phase = f[7]
143
- const attrString = f[8]
138
+ const startStr = f[3]!
139
+ const endStr = f[4]!
140
+ const scoreStr = f[5]!
141
+ const strand = f[6]!
142
+ const phase = f[7]!
143
+ const attrString = f[8]!
144
144
 
145
145
  return {
146
- seq_id: normImpl(f[0], shouldUnescape),
147
- source: normImpl(f[1], shouldUnescape),
148
- type: normImpl(f[2], shouldUnescape),
146
+ seq_id: normImpl(f[0]!, shouldUnescape),
147
+ source: normImpl(f[1]!, shouldUnescape),
148
+ type: normImpl(f[2]!, shouldUnescape),
149
149
  start: startStr.length === 0 || startStr === '.' ? null : +startStr,
150
150
  end: endStr.length === 0 || endStr === '.' ? null : +endStr,
151
151
  score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
@@ -255,26 +255,26 @@ export function parseDirective(
255
255
  const [, name] = match
256
256
  let [, , contents] = match
257
257
 
258
- const parsed: GFF3Directive = { directive: name }
259
- if (contents.length) {
260
- contents = contents.replace(lineEndRegex, '')
258
+ const parsed: GFF3Directive = { directive: name! }
259
+ if (contents!.length) {
260
+ contents = contents!.replace(lineEndRegex, '')
261
261
  parsed.value = contents
262
262
  }
263
263
 
264
264
  if (name === 'sequence-region') {
265
- const c = contents.split(whitespaceRegex, 3)
265
+ const c = contents!.split(whitespaceRegex, 3)
266
266
  return {
267
267
  ...parsed,
268
- seq_id: c[0],
269
- start: c[1]?.replaceAll(nonDigitRegex, ''),
270
- end: c[2]?.replaceAll(nonDigitRegex, ''),
268
+ seq_id: c[0]!,
269
+ start: c[1]!.replaceAll(nonDigitRegex, ''),
270
+ end: c[2]!.replaceAll(nonDigitRegex, ''),
271
271
  }
272
272
  } else if (name === 'genome-build') {
273
- const [source, buildName] = contents.split(whitespaceRegex, 2)
273
+ const [source, buildName] = contents!.split(whitespaceRegex, 2)
274
274
  return {
275
275
  ...parsed,
276
- source,
277
- buildName,
276
+ source: source!,
277
+ buildName: buildName!,
278
278
  }
279
279
  }
280
280
 
@@ -499,15 +499,15 @@ function parseFeatureJBrowseImpl(
499
499
  shouldUnescape: boolean,
500
500
  ): JBrowseFeature {
501
501
  const f = line.split('\t')
502
- const seq_id = f[0]
503
- const source = f[1]
504
- const type = f[2]
505
- const startStr = f[3]
506
- const endStr = f[4]
507
- const scoreStr = f[5]
508
- const strand = f[6]
509
- const phase = f[7]
510
- const attrString = f[8]
502
+ const seq_id = f[0]!
503
+ const source = f[1]!
504
+ const type = f[2]!
505
+ const startStr = f[3]!
506
+ const endStr = f[4]!
507
+ const scoreStr = f[5]!
508
+ const strand = f[6]!
509
+ const phase = f[7]!
510
+ const attrString = f[8]!
511
511
 
512
512
  const result: JBrowseFeature = {
513
513
  refName: