gff-nostream 3.0.0 → 3.0.1

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 (22) hide show
  1. package/dist/api.d.ts +17 -2
  2. package/dist/api.js +77 -1
  3. package/dist/api.js.map +1 -1
  4. package/dist/index.d.ts +2 -2
  5. package/dist/index.js +3 -1
  6. package/dist/index.js.map +1 -1
  7. package/dist/util.d.ts +16 -0
  8. package/dist/util.js +168 -0
  9. package/dist/util.js.map +1 -1
  10. package/esm/api.d.ts +17 -2
  11. package/esm/api.js +76 -2
  12. package/esm/api.js.map +1 -1
  13. package/esm/index.d.ts +2 -2
  14. package/esm/index.js +1 -1
  15. package/esm/index.js.map +1 -1
  16. package/esm/util.d.ts +16 -0
  17. package/esm/util.js +164 -0
  18. package/esm/util.js.map +1 -1
  19. package/package.json +1 -1
  20. package/src/api.ts +96 -3
  21. package/src/index.ts +7 -1
  22. package/src/util.ts +206 -0
package/dist/api.d.ts CHANGED
@@ -1,4 +1,4 @@
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- import type { GFF3Feature } from './util.ts';
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+ import type { GFF3Feature, JBrowseFeature } from './util.ts';
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  export interface LineRecord {
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  line: string;
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  lineHash?: string | number;
@@ -14,6 +14,13 @@ export interface LineRecord {
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  * @returns array of parsed features
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  */
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  export declare function parseStringSync(str: string): GFF3Feature[];
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+ /**
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+ * Synchronously parse a string containing GFF3 directly into JBrowse format.
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+ *
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+ * @param str - GFF3 string
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+ * @returns array of JBrowse-format features
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+ */
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+ export declare function parseStringSyncJBrowse(str: string): JBrowseFeature[];
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  /**
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  * Parse an array of LineRecord objects containing raw GFF3 lines.
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  * Supports parent/child relationships.
@@ -22,4 +29,12 @@ export declare function parseStringSync(str: string): GFF3Feature[];
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  * @returns array of parsed features
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  */
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  export declare function parseRecords(records: LineRecord[]): GFF3Feature[];
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- export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';
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+ /**
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+ * Parse an array of LineRecord objects directly into JBrowse feature format.
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+ * Supports parent/child relationships via subfeatures.
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+ *
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+ * @param records - Array of LineRecord objects with raw line and metadata
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+ * @returns array of JBrowse-format features
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+ */
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+ export declare function parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[];
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+ export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, } from './util.ts';
package/dist/api.js CHANGED
@@ -1,7 +1,9 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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  exports.parseStringSync = parseStringSync;
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+ exports.parseStringSyncJBrowse = parseStringSyncJBrowse;
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  exports.parseRecords = parseRecords;
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+ exports.parseRecordsJBrowse = parseRecordsJBrowse;
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  const util_ts_1 = require("./util.js");
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  /**
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  * Synchronously parse a string containing GFF3 and return an array of the
@@ -11,6 +13,18 @@ const util_ts_1 = require("./util.js");
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  * @returns array of parsed features
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  */
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  function parseStringSync(str) {
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+ return parseRecords(stringToRecords(str));
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+ }
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+ /**
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+ * Synchronously parse a string containing GFF3 directly into JBrowse format.
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+ *
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+ * @param str - GFF3 string
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+ * @returns array of JBrowse-format features
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+ */
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+ function parseStringSyncJBrowse(str) {
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+ return parseRecordsJBrowse(stringToRecords(str));
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+ }
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+ function stringToRecords(str) {
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  const lines = str.split(/\r?\n/);
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  const records = [];
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  for (let i = 0; i < lines.length; i++) {
@@ -31,7 +45,7 @@ function parseStringSync(str) {
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  hasEscapes: line.includes('%'),
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  });
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  }
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- return parseRecords(records);
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+ return records;
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  }
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  /**
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  * Parse an array of LineRecord objects containing raw GFF3 lines.
@@ -112,4 +126,66 @@ function parseRecords(records) {
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  }
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  return items;
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  }
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+ /**
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+ * Parse an array of LineRecord objects directly into JBrowse feature format.
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+ * Supports parent/child relationships via subfeatures.
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+ *
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+ * @param records - Array of LineRecord objects with raw line and metadata
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+ * @returns array of JBrowse-format features
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+ */
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+ function parseRecordsJBrowse(records) {
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+ const items = [];
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+ const byId = new Map();
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+ const orphans = new Map();
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+ for (let i = 0; i < records.length; i++) {
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+ const record = records[i];
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+ const feature = record.hasEscapes
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+ ? (0, util_ts_1.parseFeatureJBrowse)(record.line)
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+ : (0, util_ts_1.parseFeatureJBrowseNoUnescape)(record.line);
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+ if (record.lineHash !== undefined) {
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+ feature._lineHash = String(record.lineHash);
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+ }
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+ const id = feature.id;
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+ const parent = feature.parent;
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+ if (!id && !parent) {
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+ items.push(feature);
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+ continue;
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+ }
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+ if (id) {
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+ const existing = byId.get(id);
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+ if (!existing) {
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+ if (!parent) {
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+ items.push(feature);
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+ }
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+ byId.set(id, feature);
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+ const waiting = orphans.get(id);
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+ if (waiting) {
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+ for (let j = 0; j < waiting.length; j++) {
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+ feature.subfeatures.push(waiting[j]);
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+ }
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+ orphans.delete(id);
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+ }
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+ }
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+ }
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+ if (parent) {
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+ const parents = Array.isArray(parent) ? parent : [parent];
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+ for (let j = 0; j < parents.length; j++) {
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+ const parentId = parents[j];
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+ const parentFeature = byId.get(parentId);
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+ if (parentFeature) {
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+ parentFeature.subfeatures.push(feature);
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+ }
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+ else {
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+ let arr = orphans.get(parentId);
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+ if (!arr) {
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+ arr = [];
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+ orphans.set(parentId, arr);
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+ }
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+ arr.push(feature);
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+ }
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+ }
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+ }
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+ }
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+ return items;
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+ }
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  //# sourceMappingURL=api.js.map
package/dist/api.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/dist/index.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- export { parseRecords, parseStringSync } from './api.ts';
2
- export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';
1
+ export { parseRecords, parseRecordsJBrowse, parseStringSync, parseStringSyncJBrowse, } from './api.ts';
2
+ export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, LineRecord, } from './api.ts';
package/dist/index.js CHANGED
@@ -1,7 +1,9 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.parseStringSync = exports.parseRecords = void 0;
3
+ exports.parseStringSyncJBrowse = exports.parseStringSync = exports.parseRecordsJBrowse = exports.parseRecords = void 0;
4
4
  var api_ts_1 = require("./api.js");
5
5
  Object.defineProperty(exports, "parseRecords", { enumerable: true, get: function () { return api_ts_1.parseRecords; } });
6
+ Object.defineProperty(exports, "parseRecordsJBrowse", { enumerable: true, get: function () { return api_ts_1.parseRecordsJBrowse; } });
6
7
  Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_ts_1.parseStringSync; } });
8
+ Object.defineProperty(exports, "parseStringSyncJBrowse", { enumerable: true, get: function () { return api_ts_1.parseStringSyncJBrowse; } });
7
9
  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAAwD;AAA/C,sGAAA,YAAY,OAAA;AAAE,yGAAA,eAAe,OAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAKiB;AAJf,sGAAA,YAAY,OAAA;AACZ,6GAAA,mBAAmB,OAAA;AACnB,yGAAA,eAAe,OAAA;AACf,gHAAA,sBAAsB,OAAA"}
package/dist/util.d.ts CHANGED
@@ -136,3 +136,19 @@ export interface GFF3Sequence {
136
136
  sequence: string;
137
137
  }
138
138
  export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence;
139
+ export interface JBrowseFeature {
140
+ start: number;
141
+ end: number;
142
+ strand?: number;
143
+ type: string | null;
144
+ source: string | null;
145
+ refName: string;
146
+ phase?: number;
147
+ score?: number;
148
+ subfeatures: JBrowseFeature[];
149
+ [key: string]: unknown;
150
+ }
151
+ export declare function parseAttributesJBrowse(attrString: string, result: Record<string, unknown>): void;
152
+ export declare function parseAttributesJBrowseNoUnescape(attrString: string, result: Record<string, unknown>): void;
153
+ export declare function parseFeatureJBrowse(line: string): JBrowseFeature;
154
+ export declare function parseFeatureJBrowseNoUnescape(line: string): JBrowseFeature;
package/dist/util.js CHANGED
@@ -10,6 +10,10 @@ exports.parseFeatureNoUnescape = parseFeatureNoUnescape;
10
10
  exports.parseFieldsArray = parseFieldsArray;
11
11
  exports.parseFieldsArrayNoUnescape = parseFieldsArrayNoUnescape;
12
12
  exports.parseDirective = parseDirective;
13
+ exports.parseAttributesJBrowse = parseAttributesJBrowse;
14
+ exports.parseAttributesJBrowseNoUnescape = parseAttributesJBrowseNoUnescape;
15
+ exports.parseFeatureJBrowse = parseFeatureJBrowse;
16
+ exports.parseFeatureJBrowseNoUnescape = parseFeatureJBrowseNoUnescape;
13
17
  const escapeRegex = /%([0-9A-Fa-f]{2})/g;
14
18
  const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
15
19
  const lineEndRegex = /\r?\n$/;
@@ -292,4 +296,168 @@ function parseDirective(line) {
292
296
  }
293
297
  return parsed;
294
298
  }
299
+ // JBrowse format types and parsing functions
300
+ const JBROWSE_DEFAULT_FIELDS = new Set([
301
+ 'start',
302
+ 'end',
303
+ 'seq_id',
304
+ 'score',
305
+ 'type',
306
+ 'source',
307
+ 'phase',
308
+ 'strand',
309
+ ]);
310
+ function parseStrand(s) {
311
+ if (s === '+') {
312
+ return 1;
313
+ }
314
+ if (s === '-') {
315
+ return -1;
316
+ }
317
+ if (s === '.') {
318
+ return 0;
319
+ }
320
+ return undefined;
321
+ }
322
+ function parseAttributesJBrowse(attrString, result) {
323
+ if (attrString.length === 0 || attrString === '.') {
324
+ return;
325
+ }
326
+ let len = attrString.length;
327
+ if (attrString[len - 1] === '\n') {
328
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
329
+ attrString = attrString.slice(0, len);
330
+ }
331
+ let start = 0;
332
+ while (start < len) {
333
+ let semiIdx = attrString.indexOf(';', start);
334
+ if (semiIdx === -1) {
335
+ semiIdx = len;
336
+ }
337
+ if (semiIdx > start) {
338
+ const eqIdx = attrString.indexOf('=', start);
339
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
340
+ const tag = attrString.slice(start, eqIdx);
341
+ if (tag === '_lineHash') {
342
+ start = semiIdx + 1;
343
+ continue;
344
+ }
345
+ let key = tag.toLowerCase();
346
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
347
+ key += '2';
348
+ }
349
+ const values = [];
350
+ let valStart = eqIdx + 1;
351
+ while (valStart < semiIdx) {
352
+ let commaIdx = attrString.indexOf(',', valStart);
353
+ if (commaIdx === -1 || commaIdx > semiIdx) {
354
+ commaIdx = semiIdx;
355
+ }
356
+ if (commaIdx > valStart) {
357
+ const val = attrString.slice(valStart, commaIdx);
358
+ values.push(unescape(val));
359
+ }
360
+ valStart = commaIdx + 1;
361
+ }
362
+ result[key] = values.length === 1 ? values[0] : values;
363
+ }
364
+ }
365
+ start = semiIdx + 1;
366
+ }
367
+ }
368
+ function parseAttributesJBrowseNoUnescape(attrString, result) {
369
+ if (attrString.length === 0 || attrString === '.') {
370
+ return;
371
+ }
372
+ let len = attrString.length;
373
+ if (attrString[len - 1] === '\n') {
374
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
375
+ attrString = attrString.slice(0, len);
376
+ }
377
+ let start = 0;
378
+ while (start < len) {
379
+ let semiIdx = attrString.indexOf(';', start);
380
+ if (semiIdx === -1) {
381
+ semiIdx = len;
382
+ }
383
+ if (semiIdx > start) {
384
+ const eqIdx = attrString.indexOf('=', start);
385
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
386
+ const tag = attrString.slice(start, eqIdx);
387
+ if (tag === '_lineHash') {
388
+ start = semiIdx + 1;
389
+ continue;
390
+ }
391
+ let key = tag.toLowerCase();
392
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
393
+ key += '2';
394
+ }
395
+ const values = [];
396
+ let valStart = eqIdx + 1;
397
+ while (valStart < semiIdx) {
398
+ let commaIdx = attrString.indexOf(',', valStart);
399
+ if (commaIdx === -1 || commaIdx > semiIdx) {
400
+ commaIdx = semiIdx;
401
+ }
402
+ if (commaIdx > valStart) {
403
+ values.push(attrString.slice(valStart, commaIdx));
404
+ }
405
+ valStart = commaIdx + 1;
406
+ }
407
+ result[key] = values.length === 1 ? values[0] : values;
408
+ }
409
+ }
410
+ start = semiIdx + 1;
411
+ }
412
+ }
413
+ function parseFeatureJBrowse(line) {
414
+ const f = line.split('\t');
415
+ const seq_id = f[0];
416
+ const source = f[1];
417
+ const type = f[2];
418
+ const startStr = f[3];
419
+ const endStr = f[4];
420
+ const scoreStr = f[5];
421
+ const strand = f[6];
422
+ const phase = f[7];
423
+ const attrString = f[8];
424
+ const result = {
425
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : unescape(seq_id),
426
+ source: source.length === 0 || source === '.' ? null : unescape(source),
427
+ type: type.length === 0 || type === '.' ? null : unescape(type),
428
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
429
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
430
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
431
+ strand: parseStrand(strand),
432
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
433
+ subfeatures: [],
434
+ };
435
+ parseAttributesJBrowse(attrString, result);
436
+ return result;
437
+ }
438
+ function parseFeatureJBrowseNoUnescape(line) {
439
+ const f = line.split('\t');
440
+ const seq_id = f[0];
441
+ const source = f[1];
442
+ const type = f[2];
443
+ const startStr = f[3];
444
+ const endStr = f[4];
445
+ const scoreStr = f[5];
446
+ const strand = f[6];
447
+ const phase = f[7];
448
+ const attrString = f[8];
449
+ const result = {
450
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : seq_id,
451
+ source: source.length === 0 || source === '.' ? null : source,
452
+ type: type.length === 0 || type === '.' ? null : type,
453
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
454
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
455
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
456
+ strand: parseStrand(strand),
457
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
458
+ subfeatures: [],
459
+ };
460
+ parseAttributesJBrowseNoUnescape(attrString, result);
461
+ return result;
462
+ }
295
463
  //# sourceMappingURL=util.js.map
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/api.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import type { GFF3Feature } from './util.ts';
1
+ import type { GFF3Feature, JBrowseFeature } from './util.ts';
2
2
  export interface LineRecord {
3
3
  line: string;
4
4
  lineHash?: string | number;
@@ -14,6 +14,13 @@ export interface LineRecord {
14
14
  * @returns array of parsed features
15
15
  */
16
16
  export declare function parseStringSync(str: string): GFF3Feature[];
17
+ /**
18
+ * Synchronously parse a string containing GFF3 directly into JBrowse format.
19
+ *
20
+ * @param str - GFF3 string
21
+ * @returns array of JBrowse-format features
22
+ */
23
+ export declare function parseStringSyncJBrowse(str: string): JBrowseFeature[];
17
24
  /**
18
25
  * Parse an array of LineRecord objects containing raw GFF3 lines.
19
26
  * Supports parent/child relationships.
@@ -22,4 +29,12 @@ export declare function parseStringSync(str: string): GFF3Feature[];
22
29
  * @returns array of parsed features
23
30
  */
24
31
  export declare function parseRecords(records: LineRecord[]): GFF3Feature[];
25
- export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';
32
+ /**
33
+ * Parse an array of LineRecord objects directly into JBrowse feature format.
34
+ * Supports parent/child relationships via subfeatures.
35
+ *
36
+ * @param records - Array of LineRecord objects with raw line and metadata
37
+ * @returns array of JBrowse-format features
38
+ */
39
+ export declare function parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[];
40
+ export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, } from './util.ts';
package/esm/api.js CHANGED
@@ -1,4 +1,4 @@
1
- import { parseFeature, parseFeatureNoUnescape } from "./util.js";
1
+ import { parseFeature, parseFeatureJBrowse, parseFeatureJBrowseNoUnescape, parseFeatureNoUnescape, } from "./util.js";
2
2
  /**
3
3
  * Synchronously parse a string containing GFF3 and return an array of the
4
4
  * parsed items.
@@ -7,6 +7,18 @@ import { parseFeature, parseFeatureNoUnescape } from "./util.js";
7
7
  * @returns array of parsed features
8
8
  */
9
9
  export function parseStringSync(str) {
10
+ return parseRecords(stringToRecords(str));
11
+ }
12
+ /**
13
+ * Synchronously parse a string containing GFF3 directly into JBrowse format.
14
+ *
15
+ * @param str - GFF3 string
16
+ * @returns array of JBrowse-format features
17
+ */
18
+ export function parseStringSyncJBrowse(str) {
19
+ return parseRecordsJBrowse(stringToRecords(str));
20
+ }
21
+ function stringToRecords(str) {
10
22
  const lines = str.split(/\r?\n/);
11
23
  const records = [];
12
24
  for (let i = 0; i < lines.length; i++) {
@@ -27,7 +39,7 @@ export function parseStringSync(str) {
27
39
  hasEscapes: line.includes('%'),
28
40
  });
29
41
  }
30
- return parseRecords(records);
42
+ return records;
31
43
  }
32
44
  /**
33
45
  * Parse an array of LineRecord objects containing raw GFF3 lines.
@@ -108,4 +120,66 @@ export function parseRecords(records) {
108
120
  }
109
121
  return items;
110
122
  }
123
+ /**
124
+ * Parse an array of LineRecord objects directly into JBrowse feature format.
125
+ * Supports parent/child relationships via subfeatures.
126
+ *
127
+ * @param records - Array of LineRecord objects with raw line and metadata
128
+ * @returns array of JBrowse-format features
129
+ */
130
+ export function parseRecordsJBrowse(records) {
131
+ const items = [];
132
+ const byId = new Map();
133
+ const orphans = new Map();
134
+ for (let i = 0; i < records.length; i++) {
135
+ const record = records[i];
136
+ const feature = record.hasEscapes
137
+ ? parseFeatureJBrowse(record.line)
138
+ : parseFeatureJBrowseNoUnescape(record.line);
139
+ if (record.lineHash !== undefined) {
140
+ feature._lineHash = String(record.lineHash);
141
+ }
142
+ const id = feature.id;
143
+ const parent = feature.parent;
144
+ if (!id && !parent) {
145
+ items.push(feature);
146
+ continue;
147
+ }
148
+ if (id) {
149
+ const existing = byId.get(id);
150
+ if (!existing) {
151
+ if (!parent) {
152
+ items.push(feature);
153
+ }
154
+ byId.set(id, feature);
155
+ const waiting = orphans.get(id);
156
+ if (waiting) {
157
+ for (let j = 0; j < waiting.length; j++) {
158
+ feature.subfeatures.push(waiting[j]);
159
+ }
160
+ orphans.delete(id);
161
+ }
162
+ }
163
+ }
164
+ if (parent) {
165
+ const parents = Array.isArray(parent) ? parent : [parent];
166
+ for (let j = 0; j < parents.length; j++) {
167
+ const parentId = parents[j];
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);
179
+ }
180
+ }
181
+ }
182
+ }
183
+ return items;
184
+ }
111
185
  //# sourceMappingURL=api.js.map
package/esm/api.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAYhE;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,OAAO,GAAiB,EAAE,CAAA;IAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACzC,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,MAAK;YACP,CAAC;YACD,SAAQ;QACV,CAAC;QACD,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACpB,MAAK;QACP,CAAC;QACD,OAAO,CAAC,IAAI,CAAC;YACX,IAAI;YACJ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;YACN,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;SAC/B,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,YAAY,CAAC,OAAO,CAAC,CAAA;AAC9B,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAAC,OAAqB;IAChD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAuB,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAEhD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACxC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,WAAW,GAAG,CAClB,MAAM,CAAC,UAAU;YACf,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC;YAC3B,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QAC5B,WAAW,CAAC,cAAc,GAAG,EAAE,CAAA;QAC/B,WAAW,CAAC,gBAAgB,GAAG,EAAE,CAAA;QAEjC,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,IAAI,CAAC,WAAW,CAAC,UAAU,EAAE,CAAC;gBAC5B,WAAW,CAAC,UAAU,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED,MAAM,KAAK,GAAG,WAAW,CAAC,UAAU,CAAA;QACpC,MAAM,GAAG,GAAG,KAAK,EAAE,EAAE,CAAA;QACrB,MAAM,OAAO,GAAG,KAAK,EAAE,MAAM,CAAA;QAE7B,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;YACzB,SAAQ;QACV,CAAC;QAED,IAAI,OAAoB,CAAA;QACxB,IAAI,GAAG,EAAE,CAAC;YACR,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;YAClB,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YAC7B,IAAI,QAAQ,EAAE,CAAC;gBACb,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC1B,OAAO,GAAG,QAAQ,CAAA;YACpB,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;gBACvB,IAAI,CAAC,OAAO,EAAE,CAAC;oBACb,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACxC,WAAW,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC9C,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;QACH,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;QACzB,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxC,MAAM,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;gBAC5B,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;gBACjC,IAAI,MAAM,EAAE,CAAC;oBACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACvC,MAAM,CAAC,CAAC,CAAE,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACzC,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;wBACT,GAAG,GAAG,EAAE,CAAA;wBACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;oBAC5B,CAAC;oBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC"}
1
+ {"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,6BAA6B,EAC7B,sBAAsB,GACvB,MAAM,WAAW,CAAA;AAgBlB;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,OAAO,YAAY,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,sBAAsB,CAAC,GAAW;IAChD,OAAO,mBAAmB,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAClD,CAAC;AAED,SAAS,eAAe,CAAC,GAAW;IAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,OAAO,GAAiB,EAAE,CAAA;IAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACzC,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,MAAK;YACP,CAAC;YACD,SAAQ;QACV,CAAC;QACD,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACpB,MAAK;QACP,CAAC;QACD,OAAO,CAAC,IAAI,CAAC;YACX,IAAI;YACJ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;YACN,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;SAC/B,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,YAAY,CAAC,OAAqB;IAChD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAuB,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAEhD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACxC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,WAAW,GAAG,CAClB,MAAM,CAAC,UAAU;YACf,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC;YAC3B,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QAC5B,WAAW,CAAC,cAAc,GAAG,EAAE,CAAA;QAC/B,WAAW,CAAC,gBAAgB,GAAG,EAAE,CAAA;QAEjC,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,IAAI,CAAC,WAAW,CAAC,UAAU,EAAE,CAAC;gBAC5B,WAAW,CAAC,UAAU,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED,MAAM,KAAK,GAAG,WAAW,CAAC,UAAU,CAAA;QACpC,MAAM,GAAG,GAAG,KAAK,EAAE,EAAE,CAAA;QACrB,MAAM,OAAO,GAAG,KAAK,EAAE,MAAM,CAAA;QAE7B,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;YACzB,SAAQ;QACV,CAAC;QAED,IAAI,OAAoB,CAAA;QACxB,IAAI,GAAG,EAAE,CAAC;YACR,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;YAClB,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YAC7B,IAAI,QAAQ,EAAE,CAAC;gBACb,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC1B,OAAO,GAAG,QAAQ,CAAA;YACpB,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;gBACvB,IAAI,CAAC,OAAO,EAAE,CAAC;oBACb,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACxC,WAAW,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC9C,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;QACH,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;QACzB,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxC,MAAM,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;gBAC5B,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;gBACjC,IAAI,MAAM,EAAE,CAAC;oBACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACvC,MAAM,CAAC,CAAC,CAAE,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACzC,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;wBACT,GAAG,GAAG,EAAE,CAAA;wBACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;oBAC5B,CAAC;oBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CAAC,OAAqB;IACvD,MAAM,KAAK,GAAqB,EAAE,CAAA;IAClC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA0B,CAAA;IAC9C,MAAM,OAAO,GAAG,IAAI,GAAG,EAA4B,CAAA;IAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACxC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,OAAO,GAAG,MAAM,CAAC,UAAU;YAC/B,CAAC,CAAC,mBAAmB,CAAC,MAAM,CAAC,IAAI,CAAC;YAClC,CAAC,CAAC,6BAA6B,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAE9C,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,OAAO,CAAC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;QAC7C,CAAC;QAED,MAAM,EAAE,GAAG,OAAO,CAAC,EAAwB,CAAA;QAC3C,MAAM,MAAM,GAAG,OAAO,CAAC,MAAuC,CAAA;QAE9D,IAAI,CAAC,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC;YACnB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACnB,SAAQ;QACV,CAAC;QAED,IAAI,EAAE,EAAE,CAAC;YACP,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YAC7B,IAAI,CAAC,QAAQ,EAAE,CAAC;gBACd,IAAI,CAAC,MAAM,EAAE,CAAC;oBACZ,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACxC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAE,CAAC,CAAA;oBACvC,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;QACH,CAAC;QAED,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACxC,MAAM,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;gBAC5B,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;gBACxC,IAAI,aAAa,EAAE,CAAC;oBAClB,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;wBACT,GAAG,GAAG,EAAE,CAAA;wBACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;oBAC5B,CAAC;oBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC"}
package/esm/index.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- export { parseRecords, parseStringSync } from './api.ts';
2
- export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';
1
+ export { parseRecords, parseRecordsJBrowse, parseStringSync, parseStringSyncJBrowse, } from './api.ts';
2
+ export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, LineRecord, } from './api.ts';
package/esm/index.js CHANGED
@@ -1,2 +1,2 @@
1
- export { parseRecords, parseStringSync } from "./api.js";
1
+ export { parseRecords, parseRecordsJBrowse, parseStringSync, parseStringSyncJBrowse, } from "./api.js";
2
2
  //# sourceMappingURL=index.js.map
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,eAAe,EACf,sBAAsB,GACvB,MAAM,UAAU,CAAA"}
package/esm/util.d.ts CHANGED
@@ -136,3 +136,19 @@ export interface GFF3Sequence {
136
136
  sequence: string;
137
137
  }
138
138
  export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence;
139
+ export interface JBrowseFeature {
140
+ start: number;
141
+ end: number;
142
+ strand?: number;
143
+ type: string | null;
144
+ source: string | null;
145
+ refName: string;
146
+ phase?: number;
147
+ score?: number;
148
+ subfeatures: JBrowseFeature[];
149
+ [key: string]: unknown;
150
+ }
151
+ export declare function parseAttributesJBrowse(attrString: string, result: Record<string, unknown>): void;
152
+ export declare function parseAttributesJBrowseNoUnescape(attrString: string, result: Record<string, unknown>): void;
153
+ export declare function parseFeatureJBrowse(line: string): JBrowseFeature;
154
+ export declare function parseFeatureJBrowseNoUnescape(line: string): JBrowseFeature;
package/esm/util.js CHANGED
@@ -282,4 +282,168 @@ export function parseDirective(line) {
282
282
  }
283
283
  return parsed;
284
284
  }
285
+ // JBrowse format types and parsing functions
286
+ const JBROWSE_DEFAULT_FIELDS = new Set([
287
+ 'start',
288
+ 'end',
289
+ 'seq_id',
290
+ 'score',
291
+ 'type',
292
+ 'source',
293
+ 'phase',
294
+ 'strand',
295
+ ]);
296
+ function parseStrand(s) {
297
+ if (s === '+') {
298
+ return 1;
299
+ }
300
+ if (s === '-') {
301
+ return -1;
302
+ }
303
+ if (s === '.') {
304
+ return 0;
305
+ }
306
+ return undefined;
307
+ }
308
+ export function parseAttributesJBrowse(attrString, result) {
309
+ if (attrString.length === 0 || attrString === '.') {
310
+ return;
311
+ }
312
+ let len = attrString.length;
313
+ if (attrString[len - 1] === '\n') {
314
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
315
+ attrString = attrString.slice(0, len);
316
+ }
317
+ let start = 0;
318
+ while (start < len) {
319
+ let semiIdx = attrString.indexOf(';', start);
320
+ if (semiIdx === -1) {
321
+ semiIdx = len;
322
+ }
323
+ if (semiIdx > start) {
324
+ const eqIdx = attrString.indexOf('=', start);
325
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
326
+ const tag = attrString.slice(start, eqIdx);
327
+ if (tag === '_lineHash') {
328
+ start = semiIdx + 1;
329
+ continue;
330
+ }
331
+ let key = tag.toLowerCase();
332
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
333
+ key += '2';
334
+ }
335
+ const values = [];
336
+ let valStart = eqIdx + 1;
337
+ while (valStart < semiIdx) {
338
+ let commaIdx = attrString.indexOf(',', valStart);
339
+ if (commaIdx === -1 || commaIdx > semiIdx) {
340
+ commaIdx = semiIdx;
341
+ }
342
+ if (commaIdx > valStart) {
343
+ const val = attrString.slice(valStart, commaIdx);
344
+ values.push(unescape(val));
345
+ }
346
+ valStart = commaIdx + 1;
347
+ }
348
+ result[key] = values.length === 1 ? values[0] : values;
349
+ }
350
+ }
351
+ start = semiIdx + 1;
352
+ }
353
+ }
354
+ export function parseAttributesJBrowseNoUnescape(attrString, result) {
355
+ if (attrString.length === 0 || attrString === '.') {
356
+ return;
357
+ }
358
+ let len = attrString.length;
359
+ if (attrString[len - 1] === '\n') {
360
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1;
361
+ attrString = attrString.slice(0, len);
362
+ }
363
+ let start = 0;
364
+ while (start < len) {
365
+ let semiIdx = attrString.indexOf(';', start);
366
+ if (semiIdx === -1) {
367
+ semiIdx = len;
368
+ }
369
+ if (semiIdx > start) {
370
+ const eqIdx = attrString.indexOf('=', start);
371
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
372
+ const tag = attrString.slice(start, eqIdx);
373
+ if (tag === '_lineHash') {
374
+ start = semiIdx + 1;
375
+ continue;
376
+ }
377
+ let key = tag.toLowerCase();
378
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
379
+ key += '2';
380
+ }
381
+ const values = [];
382
+ let valStart = eqIdx + 1;
383
+ while (valStart < semiIdx) {
384
+ let commaIdx = attrString.indexOf(',', valStart);
385
+ if (commaIdx === -1 || commaIdx > semiIdx) {
386
+ commaIdx = semiIdx;
387
+ }
388
+ if (commaIdx > valStart) {
389
+ values.push(attrString.slice(valStart, commaIdx));
390
+ }
391
+ valStart = commaIdx + 1;
392
+ }
393
+ result[key] = values.length === 1 ? values[0] : values;
394
+ }
395
+ }
396
+ start = semiIdx + 1;
397
+ }
398
+ }
399
+ export function parseFeatureJBrowse(line) {
400
+ const f = line.split('\t');
401
+ const seq_id = f[0];
402
+ const source = f[1];
403
+ const type = f[2];
404
+ const startStr = f[3];
405
+ const endStr = f[4];
406
+ const scoreStr = f[5];
407
+ const strand = f[6];
408
+ const phase = f[7];
409
+ const attrString = f[8];
410
+ const result = {
411
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : unescape(seq_id),
412
+ source: source.length === 0 || source === '.' ? null : unescape(source),
413
+ type: type.length === 0 || type === '.' ? null : unescape(type),
414
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
415
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
416
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
417
+ strand: parseStrand(strand),
418
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
419
+ subfeatures: [],
420
+ };
421
+ parseAttributesJBrowse(attrString, result);
422
+ return result;
423
+ }
424
+ export function parseFeatureJBrowseNoUnescape(line) {
425
+ const f = line.split('\t');
426
+ const seq_id = f[0];
427
+ const source = f[1];
428
+ const type = f[2];
429
+ const startStr = f[3];
430
+ const endStr = f[4];
431
+ const scoreStr = f[5];
432
+ const strand = f[6];
433
+ const phase = f[7];
434
+ const attrString = f[8];
435
+ const result = {
436
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : seq_id,
437
+ source: source.length === 0 || source === '.' ? null : source,
438
+ type: type.length === 0 || type === '.' ? null : type,
439
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
440
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
441
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
442
+ strand: parseStrand(strand),
443
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
444
+ subfeatures: [],
445
+ };
446
+ parseAttributesJBrowseNoUnescape(attrString, result);
447
+ return result;
448
+ }
285
449
  //# sourceMappingURL=util.js.map
package/esm/util.js.map CHANGED
@@ -1 +1 @@
1
- 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MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC;QACvE,IAAI,EAAE,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC;QAC/D,KAAK,EAAE,QAAQ,CAAC,MAAM,KAAK,CAAC,IAAI,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC;QACpE,GAAG,EAAE,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM;QACxD,KAAK,EAAE,QAAQ,CAAC,MAAM,KAAK,CAAC,IAAI,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,QAAQ;QACxE,MAAM,EAAE,WAAW,CAAC,MAAM,CAAC;QAC3B,KAAK,EAAE,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK;QAC/D,WAAW,EAAE,EAAE;KAChB,CAAA;IAED,sBAAsB,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;IAC1C,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,IAAY;IACxD,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACpB,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACpB,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IAClB,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACtB,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACpB,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACtB,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACpB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACnB,MAAM,UAAU,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IAExB,MAAM,MAAM,GAAmB;QAC7B,OAAO,EAAE,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM;QAC5D,MAAM,EAAE,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM;QAC7D,IAAI,EAAE,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI;QACrD,KAAK,EAAE,QAAQ,CAAC,MAAM,KAAK,CAAC,IAAI,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC;QACpE,GAAG,EAAE,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM;QACxD,KAAK,EAAE,QAAQ,CAAC,MAAM,KAAK,CAAC,IAAI,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,QAAQ;QACxE,MAAM,EAAE,WAAW,CAAC,MAAM,CAAC;QAC3B,KAAK,EAAE,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK;QAC/D,WAAW,EAAE,EAAE;KAChB,CAAA;IAED,gCAAgC,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;IACpD,OAAO,MAAM,CAAA;AACf,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "gff-nostream",
3
- "version": "3.0.0",
3
+ "version": "3.0.1",
4
4
  "description": "utilities to read GFF3 data",
5
5
  "license": "MIT",
6
6
  "repository": "cmdcolin/gff-nostream",
package/src/api.ts CHANGED
@@ -1,6 +1,15 @@
1
- import { parseFeature, parseFeatureNoUnescape } from './util.ts'
1
+ import {
2
+ parseFeature,
3
+ parseFeatureJBrowse,
4
+ parseFeatureJBrowseNoUnescape,
5
+ parseFeatureNoUnescape,
6
+ } from './util.ts'
2
7
 
3
- import type { GFF3Feature, GFF3FeatureLineWithRefs } from './util.ts'
8
+ import type {
9
+ GFF3Feature,
10
+ GFF3FeatureLineWithRefs,
11
+ JBrowseFeature,
12
+ } from './util.ts'
4
13
 
5
14
  export interface LineRecord {
6
15
  line: string
@@ -18,6 +27,20 @@ export interface LineRecord {
18
27
  * @returns array of parsed features
19
28
  */
20
29
  export function parseStringSync(str: string): GFF3Feature[] {
30
+ return parseRecords(stringToRecords(str))
31
+ }
32
+
33
+ /**
34
+ * Synchronously parse a string containing GFF3 directly into JBrowse format.
35
+ *
36
+ * @param str - GFF3 string
37
+ * @returns array of JBrowse-format features
38
+ */
39
+ export function parseStringSyncJBrowse(str: string): JBrowseFeature[] {
40
+ return parseRecordsJBrowse(stringToRecords(str))
41
+ }
42
+
43
+ function stringToRecords(str: string) {
21
44
  const lines = str.split(/\r?\n/)
22
45
  const records: LineRecord[] = []
23
46
  for (let i = 0; i < lines.length; i++) {
@@ -38,7 +61,7 @@ export function parseStringSync(str: string): GFF3Feature[] {
38
61
  hasEscapes: line.includes('%'),
39
62
  })
40
63
  }
41
- return parseRecords(records)
64
+ return records
42
65
  }
43
66
 
44
67
  /**
@@ -127,6 +150,75 @@ export function parseRecords(records: LineRecord[]): GFF3Feature[] {
127
150
  return items
128
151
  }
129
152
 
153
+ /**
154
+ * Parse an array of LineRecord objects directly into JBrowse feature format.
155
+ * Supports parent/child relationships via subfeatures.
156
+ *
157
+ * @param records - Array of LineRecord objects with raw line and metadata
158
+ * @returns array of JBrowse-format features
159
+ */
160
+ export function parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[] {
161
+ const items: JBrowseFeature[] = []
162
+ const byId = new Map<string, JBrowseFeature>()
163
+ const orphans = new Map<string, JBrowseFeature[]>()
164
+
165
+ for (let i = 0; i < records.length; i++) {
166
+ const record = records[i]!
167
+ const feature = record.hasEscapes
168
+ ? parseFeatureJBrowse(record.line)
169
+ : parseFeatureJBrowseNoUnescape(record.line)
170
+
171
+ if (record.lineHash !== undefined) {
172
+ feature._lineHash = String(record.lineHash)
173
+ }
174
+
175
+ const id = feature.id as string | undefined
176
+ const parent = feature.parent as string | string[] | undefined
177
+
178
+ if (!id && !parent) {
179
+ items.push(feature)
180
+ continue
181
+ }
182
+
183
+ if (id) {
184
+ const existing = byId.get(id)
185
+ if (!existing) {
186
+ if (!parent) {
187
+ items.push(feature)
188
+ }
189
+ byId.set(id, feature)
190
+ const waiting = orphans.get(id)
191
+ if (waiting) {
192
+ for (let j = 0; j < waiting.length; j++) {
193
+ feature.subfeatures.push(waiting[j]!)
194
+ }
195
+ orphans.delete(id)
196
+ }
197
+ }
198
+ }
199
+
200
+ if (parent) {
201
+ const parents = Array.isArray(parent) ? parent : [parent]
202
+ for (let j = 0; j < parents.length; j++) {
203
+ const parentId = parents[j]!
204
+ const parentFeature = byId.get(parentId)
205
+ if (parentFeature) {
206
+ parentFeature.subfeatures.push(feature)
207
+ } else {
208
+ let arr = orphans.get(parentId)
209
+ if (!arr) {
210
+ arr = []
211
+ orphans.set(parentId, arr)
212
+ }
213
+ arr.push(feature)
214
+ }
215
+ }
216
+ }
217
+ }
218
+
219
+ return items
220
+ }
221
+
130
222
  export type {
131
223
  GFF3Comment,
132
224
  GFF3Directive,
@@ -135,4 +227,5 @@ export type {
135
227
  GFF3FeatureLineWithRefs,
136
228
  GFF3Item,
137
229
  GFF3Sequence,
230
+ JBrowseFeature,
138
231
  } from './util.ts'
package/src/index.ts CHANGED
@@ -1,4 +1,9 @@
1
- export { parseRecords, parseStringSync } from './api.ts'
1
+ export {
2
+ parseRecords,
3
+ parseRecordsJBrowse,
4
+ parseStringSync,
5
+ parseStringSyncJBrowse,
6
+ } from './api.ts'
2
7
 
3
8
  export type {
4
9
  GFF3Comment,
@@ -8,5 +13,6 @@ export type {
8
13
  GFF3FeatureLineWithRefs,
9
14
  GFF3Item,
10
15
  GFF3Sequence,
16
+ JBrowseFeature,
11
17
  LineRecord,
12
18
  } from './api.ts'
package/src/util.ts CHANGED
@@ -411,3 +411,209 @@ export interface GFF3Sequence {
411
411
  }
412
412
 
413
413
  export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence
414
+
415
+ // JBrowse format types and parsing functions
416
+
417
+ const JBROWSE_DEFAULT_FIELDS = new Set([
418
+ 'start',
419
+ 'end',
420
+ 'seq_id',
421
+ 'score',
422
+ 'type',
423
+ 'source',
424
+ 'phase',
425
+ 'strand',
426
+ ])
427
+
428
+ export interface JBrowseFeature {
429
+ start: number
430
+ end: number
431
+ strand?: number
432
+ type: string | null
433
+ source: string | null
434
+ refName: string
435
+ phase?: number
436
+ score?: number
437
+ subfeatures: JBrowseFeature[]
438
+ [key: string]: unknown
439
+ }
440
+
441
+ function parseStrand(s: string) {
442
+ if (s === '+') {
443
+ return 1
444
+ }
445
+ if (s === '-') {
446
+ return -1
447
+ }
448
+ if (s === '.') {
449
+ return 0
450
+ }
451
+ return undefined
452
+ }
453
+
454
+ export function parseAttributesJBrowse(
455
+ attrString: string,
456
+ result: Record<string, unknown>,
457
+ ) {
458
+ if (attrString.length === 0 || attrString === '.') {
459
+ return
460
+ }
461
+
462
+ let len = attrString.length
463
+ if (attrString[len - 1] === '\n') {
464
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1
465
+ attrString = attrString.slice(0, len)
466
+ }
467
+
468
+ let start = 0
469
+ while (start < len) {
470
+ let semiIdx = attrString.indexOf(';', start)
471
+ if (semiIdx === -1) {
472
+ semiIdx = len
473
+ }
474
+
475
+ if (semiIdx > start) {
476
+ const eqIdx = attrString.indexOf('=', start)
477
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
478
+ const tag = attrString.slice(start, eqIdx)
479
+ if (tag === '_lineHash') {
480
+ start = semiIdx + 1
481
+ continue
482
+ }
483
+
484
+ let key = tag.toLowerCase()
485
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
486
+ key += '2'
487
+ }
488
+
489
+ const values: string[] = []
490
+ let valStart = eqIdx + 1
491
+ while (valStart < semiIdx) {
492
+ let commaIdx = attrString.indexOf(',', valStart)
493
+ if (commaIdx === -1 || commaIdx > semiIdx) {
494
+ commaIdx = semiIdx
495
+ }
496
+ if (commaIdx > valStart) {
497
+ const val = attrString.slice(valStart, commaIdx)
498
+ values.push(unescape(val))
499
+ }
500
+ valStart = commaIdx + 1
501
+ }
502
+
503
+ result[key] = values.length === 1 ? values[0] : values
504
+ }
505
+ }
506
+ start = semiIdx + 1
507
+ }
508
+ }
509
+
510
+ export function parseAttributesJBrowseNoUnescape(
511
+ attrString: string,
512
+ result: Record<string, unknown>,
513
+ ) {
514
+ if (attrString.length === 0 || attrString === '.') {
515
+ return
516
+ }
517
+
518
+ let len = attrString.length
519
+ if (attrString[len - 1] === '\n') {
520
+ len = attrString[len - 2] === '\r' ? len - 2 : len - 1
521
+ attrString = attrString.slice(0, len)
522
+ }
523
+
524
+ let start = 0
525
+ while (start < len) {
526
+ let semiIdx = attrString.indexOf(';', start)
527
+ if (semiIdx === -1) {
528
+ semiIdx = len
529
+ }
530
+
531
+ if (semiIdx > start) {
532
+ const eqIdx = attrString.indexOf('=', start)
533
+ if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
534
+ const tag = attrString.slice(start, eqIdx)
535
+ if (tag === '_lineHash') {
536
+ start = semiIdx + 1
537
+ continue
538
+ }
539
+
540
+ let key = tag.toLowerCase()
541
+ if (JBROWSE_DEFAULT_FIELDS.has(key)) {
542
+ key += '2'
543
+ }
544
+
545
+ const values: string[] = []
546
+ let valStart = eqIdx + 1
547
+ while (valStart < semiIdx) {
548
+ let commaIdx = attrString.indexOf(',', valStart)
549
+ if (commaIdx === -1 || commaIdx > semiIdx) {
550
+ commaIdx = semiIdx
551
+ }
552
+ if (commaIdx > valStart) {
553
+ values.push(attrString.slice(valStart, commaIdx))
554
+ }
555
+ valStart = commaIdx + 1
556
+ }
557
+
558
+ result[key] = values.length === 1 ? values[0] : values
559
+ }
560
+ }
561
+ start = semiIdx + 1
562
+ }
563
+ }
564
+
565
+ export function parseFeatureJBrowse(line: string): JBrowseFeature {
566
+ const f = line.split('\t')
567
+ const seq_id = f[0]!
568
+ const source = f[1]!
569
+ const type = f[2]!
570
+ const startStr = f[3]!
571
+ const endStr = f[4]!
572
+ const scoreStr = f[5]!
573
+ const strand = f[6]!
574
+ const phase = f[7]!
575
+ const attrString = f[8]!
576
+
577
+ const result: JBrowseFeature = {
578
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : unescape(seq_id),
579
+ source: source.length === 0 || source === '.' ? null : unescape(source),
580
+ type: type.length === 0 || type === '.' ? null : unescape(type),
581
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
582
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
583
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
584
+ strand: parseStrand(strand),
585
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
586
+ subfeatures: [],
587
+ }
588
+
589
+ parseAttributesJBrowse(attrString, result)
590
+ return result
591
+ }
592
+
593
+ export function parseFeatureJBrowseNoUnescape(line: string): JBrowseFeature {
594
+ const f = line.split('\t')
595
+ const seq_id = f[0]!
596
+ const source = f[1]!
597
+ const type = f[2]!
598
+ const startStr = f[3]!
599
+ const endStr = f[4]!
600
+ const scoreStr = f[5]!
601
+ const strand = f[6]!
602
+ const phase = f[7]!
603
+ const attrString = f[8]!
604
+
605
+ const result: JBrowseFeature = {
606
+ refName: seq_id.length === 0 || seq_id === '.' ? '' : seq_id,
607
+ source: source.length === 0 || source === '.' ? null : source,
608
+ type: type.length === 0 || type === '.' ? null : type,
609
+ start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
610
+ end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
611
+ score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
612
+ strand: parseStrand(strand),
613
+ phase: phase.length === 0 || phase === '.' ? undefined : +phase,
614
+ subfeatures: [],
615
+ }
616
+
617
+ parseAttributesJBrowseNoUnescape(attrString, result)
618
+ return result
619
+ }