gff-nostream 3.0.5 → 3.0.8

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Files changed (16) hide show
  1. package/README.md +63 -10
  2. package/dist/api.d.ts +4 -2
  3. package/dist/api.js +65 -63
  4. package/dist/api.js.map +1 -1
  5. package/dist/util.d.ts +0 -15
  6. package/dist/util.js +33 -97
  7. package/dist/util.js.map +1 -1
  8. package/esm/api.d.ts +4 -2
  9. package/esm/api.js +65 -63
  10. package/esm/api.js.map +1 -1
  11. package/esm/util.d.ts +0 -15
  12. package/esm/util.js +33 -95
  13. package/esm/util.js.map +1 -1
  14. package/package.json +5 -5
  15. package/src/api.ts +67 -67
  16. package/src/util.ts +46 -120
package/README.md CHANGED
@@ -3,11 +3,12 @@
3
3
  [![NPM version](https://img.shields.io/npm/v/gff-nostream.svg?style=flat-square)](https://npmjs.org/package/gff-nostream)
4
4
  [![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/gff-nostream/push.yml?branch=main)](https://github.com/GMOD/gff-nostream/actions?query=branch%3Amain+workflow%3APush+)
5
5
 
6
- Parse GFF3 data. A simplified version of [@gmod/gff](https://github.com/GMOD/gff-js) with no Node.js stream dependency.
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+ Parse GFF3 data. A simplified version of
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+ [@gmod/gff](https://github.com/GMOD/gff-js) with no Node.js stream dependency.
7
8
 
8
9
  ## Install
9
10
 
10
- $ npm install gff-nostream
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+ $ pnpm add gff-nostream
11
12
 
12
13
  ## Usage
13
14
 
@@ -15,13 +16,25 @@ Parse GFF3 data. A simplified version of [@gmod/gff](https://github.com/GMOD/gff
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16
  import { parseStringSync } from 'gff-nostream'
16
17
  import fs from 'fs'
17
18
 
18
- const stringOfGFF3 = fs.readFileSync('my_annotations.gff3', 'utf8')
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- const features = parseStringSync(stringOfGFF3)
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+ const features = parseStringSync(fs.readFileSync('my_annotations.gff3', 'utf8'))
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+ ```
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+
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+ For browser or other non-Node environments, pass any GFF3 string directly — for
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+ example from `fetch`:
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+
25
+ ```js
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+ import { parseStringSyncJBrowse } from 'gff-nostream'
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+
28
+ const text = await fetch('my_annotations.gff3').then(r => r.text())
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+ const features = parseStringSyncJBrowse(text)
20
30
  ```
21
31
 
22
32
  ## Object format
23
33
 
24
- 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.
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+ ### GFF3 format
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+
36
+ Features are returned as arrays of all lines sharing the same ID (to represent
37
+ multi-location features). Values that are `.` in GFF3 are `null` in the output.
25
38
 
26
39
  A simple feature located in one place:
27
40
 
@@ -85,28 +98,68 @@ A CDS called `cds00001` located in two places:
85
98
  ]
86
99
  ```
87
100
 
101
+ ### JBrowse format
102
+
103
+ The `JBrowse` variants return flat objects with coordinates converted to 0-based
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+ half-open, `strand` as a number (`1`/`-1`/`0`), attributes spread as lowercase
105
+ top-level keys, and `subfeatures` instead of `child_features`.
106
+
107
+ The same gene feature in JBrowse format:
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+
109
+ ```json
110
+ {
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+ "refName": "ctg123",
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+ "source": null,
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+ "type": "gene",
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+ "start": 999,
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+ "end": 9000,
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+ "strand": 1,
117
+ "subfeatures": [],
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+ "id": "gene00001",
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+ "name": "EDEN"
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+ }
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+ ```
122
+
123
+ Note: multi-location features (same ID on multiple lines) are not merged in
124
+ JBrowse format — only the first occurrence is kept.
125
+
88
126
  ## API
89
127
 
90
128
  ### `parseStringSync(str: string): GFF3Feature[]`
91
129
 
92
- Synchronously parse a GFF3 string and return an array of features.
130
+ Synchronously parse a GFF3 string and return an array of features. Comments,
131
+ directives, and `##FASTA` sections are ignored.
93
132
 
94
133
  ### `parseStringSyncJBrowse(str: string): JBrowseFeature[]`
95
134
 
96
- Synchronously parse a GFF3 string and return features in JBrowse format (flat objects with `subfeatures` instead of `child_features`).
135
+ Synchronously parse a GFF3 string and return features in JBrowse format.
97
136
 
98
137
  ### `parseRecords(records: LineRecord[]): GFF3Feature[]`
99
138
 
100
- Parse an array of `LineRecord` objects. Useful when managing raw line data directly (e.g. from an indexed file with byte offsets).
139
+ Parse an array of `LineRecord` objects. Useful when managing raw line data
140
+ directly (e.g. from a tabix-indexed file with byte offsets).
101
141
 
102
142
  ### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
103
143
 
104
144
  Same as `parseRecords` but returns JBrowse-format features.
105
145
 
146
+ ### `LineRecord`
147
+
148
+ ```ts
149
+ interface LineRecord {
150
+ line: string
151
+ hasEscapes: boolean // set true when line contains '%' to enable URL-decoding
152
+ lineHash?: string | number // propagated to attributes._lineHash on the parsed feature
153
+ start?: number // byte offset passthrough (not used by the parser)
154
+ end?: number // byte offset passthrough (not used by the parser)
155
+ }
156
+ ```
157
+
106
158
  ## Publishing
107
159
 
108
- [Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
160
+ [Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
161
+ Actions.
109
162
 
110
163
  ```bash
111
- npm version patch # or minor/major
164
+ pnpm version patch # or minor/major
112
165
  ```
package/dist/api.d.ts CHANGED
@@ -2,8 +2,10 @@ import type { GFF3Feature, JBrowseFeature } from './util.ts';
2
2
  export interface LineRecord {
3
3
  line: string;
4
4
  lineHash?: string | number;
5
- start: number;
6
- end: number;
5
+ /** Optional passthrough byte offsets — not used by the parser */
6
+ start?: number;
7
+ /** Optional passthrough byte offsets — not used by the parser */
8
+ end?: number;
7
9
  hasEscapes: boolean;
8
10
  }
9
11
  /**
package/dist/api.js CHANGED
@@ -28,19 +28,14 @@ function stringToRecords(str) {
28
28
  const lines = str.split(/\r?\n/);
29
29
  const records = [];
30
30
  for (const line of lines) {
31
+ if (line.startsWith('##FASTA') || line.startsWith('>')) {
32
+ break;
33
+ }
31
34
  if (line.length === 0 || line.startsWith('#')) {
32
- if (line.startsWith('##FASTA')) {
33
- break;
34
- }
35
35
  continue;
36
36
  }
37
- if (line.startsWith('>')) {
38
- break;
39
- }
40
37
  records.push({
41
38
  line,
42
- start: 0,
43
- end: 0,
44
39
  hasEscapes: line.includes('%'),
45
40
  });
46
41
  }
@@ -72,49 +67,55 @@ function parseRecords(records) {
72
67
  const parents = attrs?.Parent;
73
68
  if (!ids && !parents) {
74
69
  items.push([featureLine]);
75
- continue;
76
70
  }
77
- let feature;
78
- if (ids) {
79
- const id = ids[0];
80
- const existing = byId.get(id);
81
- if (existing) {
82
- existing.push(featureLine);
83
- feature = existing;
84
- }
85
- else {
86
- feature = [featureLine];
87
- if (!parents) {
88
- items.push(feature);
71
+ else {
72
+ let feature;
73
+ if (ids) {
74
+ const id = ids[0];
75
+ const existing = byId.get(id);
76
+ if (existing) {
77
+ // Multi-location continuation: share child_features/derived_features
78
+ // with the first line so children remain visible across all lines
79
+ // regardless of arrival order.
80
+ featureLine.child_features = existing[0].child_features;
81
+ featureLine.derived_features = existing[0].derived_features;
82
+ existing.push(featureLine);
83
+ feature = existing;
89
84
  }
90
- byId.set(id, feature);
91
- const waiting = orphans.get(id);
92
- if (waiting) {
93
- for (const w of waiting) {
94
- featureLine.child_features.push(w);
85
+ else {
86
+ feature = [featureLine];
87
+ if (!parents) {
88
+ items.push(feature);
89
+ }
90
+ byId.set(id, feature);
91
+ const waiting = orphans.get(id);
92
+ if (waiting) {
93
+ for (const w of waiting) {
94
+ featureLine.child_features.push(w);
95
+ }
96
+ orphans.delete(id);
95
97
  }
96
- orphans.delete(id);
97
98
  }
98
99
  }
99
- }
100
- else {
101
- feature = [featureLine];
102
- }
103
- if (parents) {
104
- for (const parentId of parents) {
105
- const parent = byId.get(parentId);
106
- if (parent) {
107
- for (const p of parent) {
108
- p.child_features.push(feature);
100
+ else {
101
+ feature = [featureLine];
102
+ }
103
+ if (parents) {
104
+ for (const parentId of parents) {
105
+ const parent = byId.get(parentId);
106
+ if (parent) {
107
+ // child_features is shared across all parent feature lines,
108
+ // so push once via the first line.
109
+ parent[0].child_features.push(feature);
109
110
  }
110
- }
111
- else {
112
- let arr = orphans.get(parentId);
113
- if (!arr) {
114
- arr = [];
115
- orphans.set(parentId, arr);
111
+ else {
112
+ let arr = orphans.get(parentId);
113
+ if (!arr) {
114
+ arr = [];
115
+ orphans.set(parentId, arr);
116
+ }
117
+ arr.push(feature);
116
118
  }
117
- arr.push(feature);
118
119
  }
119
120
  }
120
121
  }
@@ -139,15 +140,16 @@ function parseRecordsJBrowse(records) {
139
140
  if (record.lineHash !== undefined) {
140
141
  feature._lineHash = String(record.lineHash);
141
142
  }
142
- const id = feature.id;
143
+ // attribute parsing collapses single-element arrays to scalars, so id can
144
+ // be string | string[]; defensively take the first if multi-valued.
145
+ const rawId = feature.id;
146
+ const id = Array.isArray(rawId) ? rawId[0] : rawId;
143
147
  const parent = feature.parent;
144
148
  if (!id && !parent) {
145
149
  items.push(feature);
146
- continue;
147
150
  }
148
- if (id) {
149
- const existing = byId.get(id);
150
- if (!existing) {
151
+ else if (!id || !byId.has(id)) {
152
+ if (id) {
151
153
  if (!parent) {
152
154
  items.push(feature);
153
155
  }
@@ -160,21 +162,21 @@ function parseRecordsJBrowse(records) {
160
162
  orphans.delete(id);
161
163
  }
162
164
  }
163
- }
164
- if (parent) {
165
- const parents = Array.isArray(parent) ? parent : [parent];
166
- for (const parentId of parents) {
167
- const parentFeature = byId.get(parentId);
168
- if (parentFeature) {
169
- parentFeature.subfeatures.push(feature);
170
- }
171
- else {
172
- let arr = orphans.get(parentId);
173
- if (!arr) {
174
- arr = [];
175
- orphans.set(parentId, arr);
165
+ if (parent) {
166
+ const parents = Array.isArray(parent) ? parent : [parent];
167
+ for (const parentId of parents) {
168
+ const parentFeature = byId.get(parentId);
169
+ if (parentFeature) {
170
+ parentFeature.subfeatures.push(feature);
171
+ }
172
+ else {
173
+ let arr = orphans.get(parentId);
174
+ if (!arr) {
175
+ arr = [];
176
+ orphans.set(parentId, arr);
177
+ }
178
+ arr.push(feature);
176
179
  }
177
- arr.push(feature);
178
180
  }
179
181
  }
180
182
  }
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1
+ 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package/dist/util.d.ts CHANGED
@@ -35,21 +35,6 @@ export declare function parseFeature(line: string): GFF3FeatureLine;
35
35
  * @returns The parsed feature
36
36
  */
37
37
  export declare function parseFeatureNoUnescape(line: string): GFF3FeatureLine;
38
- /**
39
- * Parse a GFF3 feature from a pre-split fields array
40
- *
41
- * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
42
- * @returns The parsed feature
43
- */
44
- export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
45
- /**
46
- * Parse a GFF3 feature from a pre-split fields array without unescaping.
47
- * Fast path for data known to contain no escaped characters.
48
- *
49
- * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
50
- * @returns The parsed feature
51
- */
52
- export declare function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine;
53
38
  /**
54
39
  * Parse a GFF3 directive line.
55
40
  *
package/dist/util.js CHANGED
@@ -7,15 +7,12 @@ exports.parseAttributes = parseAttributes;
7
7
  exports.parseAttributesNoUnescape = parseAttributesNoUnescape;
8
8
  exports.parseFeature = parseFeature;
9
9
  exports.parseFeatureNoUnescape = parseFeatureNoUnescape;
10
- exports.parseFieldsArray = parseFieldsArray;
11
- exports.parseFieldsArrayNoUnescape = parseFieldsArrayNoUnescape;
12
10
  exports.parseDirective = parseDirective;
13
11
  exports.parseAttributesJBrowse = parseAttributesJBrowse;
14
12
  exports.parseAttributesJBrowseNoUnescape = parseAttributesJBrowseNoUnescape;
15
13
  exports.parseFeatureJBrowse = parseFeatureJBrowse;
16
14
  exports.parseFeatureJBrowseNoUnescape = parseFeatureJBrowseNoUnescape;
17
15
  const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
18
- const lineEndRegex = /\r?\n$/;
19
16
  const whitespaceRegex = /\s+/;
20
17
  const nonDigitRegex = /\D/g;
21
18
  const HEX_LOOKUP = {};
@@ -120,30 +117,28 @@ function parseAttributes(attrString) {
120
117
  function parseAttributesNoUnescape(attrString) {
121
118
  return parseAttributesImpl(attrString, false);
122
119
  }
123
- function normImpl(s, shouldUnescape) {
124
- if (s.length === 0 || s === '.') {
125
- return null;
126
- }
127
- return shouldUnescape ? unescape(s) : s;
120
+ function isEmpty(s) {
121
+ return s.length === 0 || s === '.';
122
+ }
123
+ function strField(s, shouldUnescape, empty) {
124
+ return isEmpty(s) ? empty : shouldUnescape ? unescape(s) : s;
125
+ }
126
+ function numField(s) {
127
+ return isEmpty(s) ? null : +s;
128
128
  }
129
129
  function parseFeatureImpl(line, shouldUnescape) {
130
130
  const f = line.split('\t');
131
- const startStr = f[3];
132
- const endStr = f[4];
133
- const scoreStr = f[5];
134
- const strand = f[6];
135
- const phase = f[7];
136
131
  const attrString = f[8];
137
132
  return {
138
- seq_id: normImpl(f[0], shouldUnescape),
139
- source: normImpl(f[1], shouldUnescape),
140
- type: normImpl(f[2], shouldUnescape),
141
- start: startStr.length === 0 || startStr === '.' ? null : +startStr,
142
- end: endStr.length === 0 || endStr === '.' ? null : +endStr,
143
- score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
144
- strand: normImpl(strand, false),
145
- phase: normImpl(phase, false),
146
- attributes: attrString.length === 0 || attrString === '.'
133
+ seq_id: strField(f[0], shouldUnescape, null),
134
+ source: strField(f[1], shouldUnescape, null),
135
+ type: strField(f[2], shouldUnescape, null),
136
+ start: numField(f[3]),
137
+ end: numField(f[4]),
138
+ score: numField(f[5]),
139
+ strand: strField(f[6], false, null),
140
+ phase: strField(f[7], false, null),
141
+ attributes: isEmpty(attrString)
147
142
  ? null
148
143
  : parseAttributesImpl(attrString, shouldUnescape),
149
144
  };
@@ -167,49 +162,6 @@ function parseFeature(line) {
167
162
  function parseFeatureNoUnescape(line) {
168
163
  return parseFeatureImpl(line, false);
169
164
  }
170
- function parseFieldsArrayImpl(f, shouldUnescape) {
171
- const seq_id = f[0];
172
- const source = f[1];
173
- const type = f[2];
174
- const startStr = f[3];
175
- const endStr = f[4];
176
- const scoreStr = f[5];
177
- const strand = f[6];
178
- const phase = f[7];
179
- const attrString = f[8];
180
- return {
181
- seq_id: seq_id ? normImpl(seq_id, shouldUnescape) : null,
182
- source: source ? normImpl(source, shouldUnescape) : null,
183
- type: type ? normImpl(type, shouldUnescape) : null,
184
- start: !startStr || startStr === '.' ? null : +startStr,
185
- end: !endStr || endStr === '.' ? null : +endStr,
186
- score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
187
- strand: strand && strand !== '.' ? strand : null,
188
- phase: phase && phase !== '.' ? phase : null,
189
- attributes: !attrString || attrString === '.'
190
- ? null
191
- : parseAttributesImpl(attrString, shouldUnescape),
192
- };
193
- }
194
- /**
195
- * Parse a GFF3 feature from a pre-split fields array
196
- *
197
- * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
198
- * @returns The parsed feature
199
- */
200
- function parseFieldsArray(f) {
201
- return parseFieldsArrayImpl(f, true);
202
- }
203
- /**
204
- * Parse a GFF3 feature from a pre-split fields array without unescaping.
205
- * Fast path for data known to contain no escaped characters.
206
- *
207
- * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
208
- * @returns The parsed feature
209
- */
210
- function parseFieldsArrayNoUnescape(f) {
211
- return parseFieldsArrayImpl(f, false);
212
- }
213
165
  /**
214
166
  * Parse a GFF3 directive line.
215
167
  *
@@ -221,12 +173,11 @@ function parseDirective(line) {
221
173
  if (!match) {
222
174
  return null;
223
175
  }
224
- const [, name] = match;
225
- let [, , contents] = match;
176
+ const name = match[1];
177
+ const contents = match[2];
226
178
  const parsed = { directive: name };
227
179
  if (contents.length) {
228
- contents = contents.replace(lineEndRegex, '');
229
- parsed.value = contents;
180
+ parsed.value = contents.trimEnd();
230
181
  }
231
182
  if (name === 'sequence-region') {
232
183
  const c = contents.split(whitespaceRegex, 3);
@@ -300,10 +251,6 @@ function parseAttributesJBrowseImpl(attrString, result, shouldUnescape) {
300
251
  const eqIdx = attrString.indexOf('=', start);
301
252
  if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
302
253
  const tag = attrString.slice(start, eqIdx);
303
- if (tag === '_lineHash') {
304
- start = semiIdx + 1;
305
- continue;
306
- }
307
254
  let key = COMMON_ATTRS[tag];
308
255
  if (key === undefined) {
309
256
  key = tag.toLowerCase();
@@ -336,38 +283,27 @@ function parseAttributesJBrowse(attrString, result) {
336
283
  function parseAttributesJBrowseNoUnescape(attrString, result) {
337
284
  parseAttributesJBrowseImpl(attrString, result, false);
338
285
  }
286
+ const STRAND_MAP = {
287
+ '+': 1,
288
+ '-': -1,
289
+ '.': 0,
290
+ };
339
291
  function parseFeatureJBrowseImpl(line, shouldUnescape) {
340
292
  const f = line.split('\t');
341
- const seq_id = f[0];
342
- const source = f[1];
343
- const type = f[2];
344
293
  const startStr = f[3];
345
294
  const endStr = f[4];
346
295
  const scoreStr = f[5];
347
- const strand = f[6];
348
296
  const phase = f[7];
349
297
  const attrString = f[8];
350
298
  const result = {
351
- refName: seq_id.length === 0 || seq_id === '.'
352
- ? ''
353
- : shouldUnescape
354
- ? unescape(seq_id)
355
- : seq_id,
356
- source: source.length === 0 || source === '.'
357
- ? null
358
- : shouldUnescape
359
- ? unescape(source)
360
- : source,
361
- type: type.length === 0 || type === '.'
362
- ? null
363
- : shouldUnescape
364
- ? unescape(type)
365
- : type,
366
- start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
367
- end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
368
- score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
369
- strand: strand === '+' ? 1 : strand === '-' ? -1 : strand === '.' ? 0 : undefined,
370
- phase: phase.length === 0 || phase === '.' ? undefined : +phase,
299
+ refName: strField(f[0], shouldUnescape, ''),
300
+ source: strField(f[1], shouldUnescape, null),
301
+ type: strField(f[2], shouldUnescape, null),
302
+ start: isEmpty(startStr) ? 0 : +startStr - 1,
303
+ end: isEmpty(endStr) ? 0 : +endStr,
304
+ score: isEmpty(scoreStr) ? undefined : +scoreStr,
305
+ strand: STRAND_MAP[f[6]],
306
+ phase: isEmpty(phase) ? undefined : +phase,
371
307
  subfeatures: [],
372
308
  };
373
309
  parseAttributesJBrowseImpl(attrString, result, shouldUnescape);
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/api.d.ts CHANGED
@@ -2,8 +2,10 @@ import type { GFF3Feature, JBrowseFeature } from './util.ts';
2
2
  export interface LineRecord {
3
3
  line: string;
4
4
  lineHash?: string | number;
5
- start: number;
6
- end: number;
5
+ /** Optional passthrough byte offsets — not used by the parser */
6
+ start?: number;
7
+ /** Optional passthrough byte offsets — not used by the parser */
8
+ end?: number;
7
9
  hasEscapes: boolean;
8
10
  }
9
11
  /**