@jbrowse/plugin-gff3 2.14.0 → 2.15.1

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Files changed (9) hide show
  1. package/dist/Gff3Adapter/Gff3Adapter.js +4 -11
  2. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +0 -1
  3. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +13 -24
  4. package/dist/featureData.d.ts +1 -1
  5. package/esm/Gff3Adapter/Gff3Adapter.js +4 -11
  6. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +0 -1
  7. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +13 -24
  8. package/esm/featureData.d.ts +1 -1
  9. package/package.json +5 -5
package/dist/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -9,7 +9,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
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  const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
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  const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
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  const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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- const gff_1 = __importDefault(require("@gmod/gff"));
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+ const gff_nostream_1 = require("gff-nostream");
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  const util_1 = require("@jbrowse/core/util");
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  const featureData_1 = require("../featureData");
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  class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -30,8 +30,8 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  let i = 0;
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  while (blockStart < buffer.length) {
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  const n = buffer.indexOf('\n', blockStart);
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- // could be a non-newline ended file, so slice to end of file if n===-1
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- const b = n === -1 ? buffer.slice(blockStart) : buffer.slice(blockStart, n);
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+ // could be a non-newline ended file, so subarray to end of file if n===-1
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+ const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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  const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
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  if (line) {
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  if (line.startsWith('#')) {
@@ -60,14 +60,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (!this.calculatedIntervalTreeMap[refName]) {
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
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  const intervalTree = new interval_tree_1.default();
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- gff_1.default
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- .parseStringSync(lines, {
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- parseFeatures: true,
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- parseComments: false,
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- parseDirectives: false,
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- parseSequences: false,
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- disableDerivesFromReferences: true,
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- })
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+ (0, gff_nostream_1.parseStringSync)(lines)
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  .flat()
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  .map((f, i) => new simpleFeature_1.default({
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  data: (0, featureData_1.featureData)(f),
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -14,6 +14,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  private getFeaturesHelper;
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  private parseLine;
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- private formatFeatures;
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  freeResources(): void;
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  }
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -9,7 +9,7 @@ const io_1 = require("@jbrowse/core/util/io");
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  const rxjs_1 = require("@jbrowse/core/util/rxjs");
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  const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
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  const tabix_1 = require("@gmod/tabix");
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- const gff_1 = __importDefault(require("@gmod/gff"));
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+ const gff_nostream_1 = require("gff-nostream");
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const featureData_1 = require("../featureData");
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  class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -45,6 +45,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }, opts.signal);
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  }
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  async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
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+ var _a, _b;
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  try {
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  const lines = [];
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  await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
@@ -53,7 +54,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (allowRedispatch && lines.length) {
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  let minStart = Number.POSITIVE_INFINITY;
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  let maxEnd = Number.NEGATIVE_INFINITY;
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- lines.forEach(line => {
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+ for (const line of lines) {
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  const featureType = line.fields[2];
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  // only expand redispatch range if feature is not a "dontRedispatch"
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  // type skips large regions like chromosome,region
@@ -66,7 +67,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  maxEnd = line.end;
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  }
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  }
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- });
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+ }
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  if (maxEnd > query.end || minStart < query.start) {
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  // make a new feature callback to only return top-level features
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  // in the original query range
@@ -75,7 +76,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  }
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  const gff3 = lines
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- .map((lineRecord) => {
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+ .map(lineRecord => {
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  if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
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  if (!lineRecord.fields[8].includes('_lineHash')) {
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  lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
@@ -87,20 +88,17 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  return lineRecord.fields.join('\t');
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  })
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  .join('\n');
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- const features = gff_1.default.parseStringSync(gff3, {
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- parseFeatures: true,
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- parseComments: false,
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- parseDirectives: false,
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- parseSequences: false,
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- disableDerivesFromReferences: true,
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- });
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- features.forEach(featureLocs => {
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- this.formatFeatures(featureLocs).forEach(f => {
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+ for (const featureLocs of (0, gff_nostream_1.parseStringSync)(gff3)) {
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+ for (const featureLoc of featureLocs) {
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+ const f = new simpleFeature_1.default({
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+ data: (0, featureData_1.featureData)(featureLoc),
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+ id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
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+ });
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  if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
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  observer.next(f);
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  }
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- });
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- });
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+ }
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+ }
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  observer.complete();
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  }
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  catch (e) {
@@ -117,15 +115,6 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  fields,
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  };
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  }
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- formatFeatures(featureLocs) {
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- return featureLocs.map(featureLoc => {
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- var _a, _b;
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- return new simpleFeature_1.default({
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- data: (0, featureData_1.featureData)(featureLoc),
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- id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
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- });
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- });
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- }
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  freeResources( /* { region } */) { }
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  }
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  exports.default = Gff3TabixAdapter;
package/dist/featureData.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- import { GFF3FeatureLineWithRefs } from '@gmod/gff';
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+ import { GFF3FeatureLineWithRefs } from 'gff-nostream';
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  export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;
package/esm/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -4,7 +4,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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  import IntervalTree from '@flatten-js/interval-tree';
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  import SimpleFeature from '@jbrowse/core/util/simpleFeature';
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  import { unzip } from '@gmod/bgzf-filehandle';
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- import gff from '@gmod/gff';
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+ import { parseStringSync } from 'gff-nostream';
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  import { isGzip, updateStatus } from '@jbrowse/core/util';
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  import { featureData } from '../featureData';
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  export default class Gff3Adapter extends BaseFeatureDataAdapter {
@@ -25,8 +25,8 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  let i = 0;
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  while (blockStart < buffer.length) {
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  const n = buffer.indexOf('\n', blockStart);
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- // could be a non-newline ended file, so slice to end of file if n===-1
29
- const b = n === -1 ? buffer.slice(blockStart) : buffer.slice(blockStart, n);
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+ // could be a non-newline ended file, so subarray to end of file if n===-1
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+ const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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  const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
31
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  if (line) {
32
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  if (line.startsWith('#')) {
@@ -55,14 +55,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
55
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  if (!this.calculatedIntervalTreeMap[refName]) {
56
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
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  const intervalTree = new IntervalTree();
58
- gff
59
- .parseStringSync(lines, {
60
- parseFeatures: true,
61
- parseComments: false,
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- parseDirectives: false,
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- parseSequences: false,
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- disableDerivesFromReferences: true,
65
- })
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+ parseStringSync(lines)
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  .flat()
67
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  .map((f, i) => new SimpleFeature({
68
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  data: featureData(f),
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -14,6 +14,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
14
14
  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
15
15
  private getFeaturesHelper;
16
16
  private parseLine;
17
- private formatFeatures;
18
17
  freeResources(): void;
19
18
  }
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -4,7 +4,7 @@ import { openLocation } from '@jbrowse/core/util/io';
4
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
5
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  import SimpleFeature from '@jbrowse/core/util/simpleFeature';
6
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  import { TabixIndexedFile } from '@gmod/tabix';
7
- import gff from '@gmod/gff';
7
+ import { parseStringSync } from 'gff-nostream';
8
8
  import { readConfObject, } from '@jbrowse/core/configuration';
9
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  import { featureData } from '../featureData';
10
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  export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
@@ -40,6 +40,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
40
40
  }, opts.signal);
41
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  }
42
42
  async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
43
+ var _a, _b;
43
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  try {
44
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  const lines = [];
45
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  await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
@@ -48,7 +49,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
48
49
  if (allowRedispatch && lines.length) {
49
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  let minStart = Number.POSITIVE_INFINITY;
50
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  let maxEnd = Number.NEGATIVE_INFINITY;
51
- lines.forEach(line => {
52
+ for (const line of lines) {
52
53
  const featureType = line.fields[2];
53
54
  // only expand redispatch range if feature is not a "dontRedispatch"
54
55
  // type skips large regions like chromosome,region
@@ -61,7 +62,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
61
62
  maxEnd = line.end;
62
63
  }
63
64
  }
64
- });
65
+ }
65
66
  if (maxEnd > query.end || minStart < query.start) {
66
67
  // make a new feature callback to only return top-level features
67
68
  // in the original query range
@@ -70,7 +71,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
70
71
  }
71
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  }
72
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  const gff3 = lines
73
- .map((lineRecord) => {
74
+ .map(lineRecord => {
74
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  if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
75
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  if (!lineRecord.fields[8].includes('_lineHash')) {
76
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  lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
@@ -82,20 +83,17 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
82
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  return lineRecord.fields.join('\t');
83
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  })
84
85
  .join('\n');
85
- const features = gff.parseStringSync(gff3, {
86
- parseFeatures: true,
87
- parseComments: false,
88
- parseDirectives: false,
89
- parseSequences: false,
90
- disableDerivesFromReferences: true,
91
- });
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- features.forEach(featureLocs => {
93
- this.formatFeatures(featureLocs).forEach(f => {
86
+ for (const featureLocs of parseStringSync(gff3)) {
87
+ for (const featureLoc of featureLocs) {
88
+ const f = new SimpleFeature({
89
+ data: featureData(featureLoc),
90
+ id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
91
+ });
94
92
  if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
95
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  observer.next(f);
96
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  }
97
- });
98
- });
95
+ }
96
+ }
99
97
  observer.complete();
100
98
  }
101
99
  catch (e) {
@@ -112,14 +110,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
112
110
  fields,
113
111
  };
114
112
  }
115
- formatFeatures(featureLocs) {
116
- return featureLocs.map(featureLoc => {
117
- var _a, _b;
118
- return new SimpleFeature({
119
- data: featureData(featureLoc),
120
- id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
121
- });
122
- });
123
- }
124
113
  freeResources( /* { region } */) { }
125
114
  }
package/esm/featureData.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- import { GFF3FeatureLineWithRefs } from '@gmod/gff';
1
+ import { GFF3FeatureLineWithRefs } from 'gff-nostream';
2
2
  export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gff3",
3
- "version": "2.14.0",
3
+ "version": "2.15.1",
4
4
  "description": "JBrowse 2 gff3.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -38,13 +38,13 @@
38
38
  "dependencies": {
39
39
  "@flatten-js/interval-tree": "^1.0.15",
40
40
  "@gmod/bgzf-filehandle": "^1.4.3",
41
- "@gmod/gff": "^1.3.0",
42
- "@gmod/tabix": "^1.5.6"
41
+ "@gmod/tabix": "^1.5.6",
42
+ "gff-nostream": "^1.3.3"
43
43
  },
44
44
  "peerDependencies": {
45
45
  "@jbrowse/core": "^2.0.0",
46
46
  "@jbrowse/plugin-linear-genome-view": "^2.0.0",
47
- "@mui/material": "^5.0.0",
47
+ "@mui/material": "^6.0.0",
48
48
  "mobx": "^6.0.0",
49
49
  "mobx-state-tree": "^5.0.0",
50
50
  "rxjs": "^7.0.0"
@@ -55,5 +55,5 @@
55
55
  "distModule": "esm/index.js",
56
56
  "srcModule": "src/index.ts",
57
57
  "module": "esm/index.js",
58
- "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
58
+ "gitHead": "86ed70124fc5a0b1161266659d1ca9f8796bf3fe"
59
59
  }