@jbrowse/plugin-gtf 3.1.0 → 3.2.0

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Files changed (3) hide show
  1. package/dist/GtfAdapter/GtfAdapter.js +7 -6
  2. package/esm/GtfAdapter/GtfAdapter.js +8 -7
  3. package/package.json +4 -4
package/dist/GtfAdapter/GtfAdapter.js CHANGED
@@ -45,7 +45,7 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  }
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  if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
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+ statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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  }
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  blockStart = n + 1;
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  }
@@ -55,10 +55,11 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (!this.calculatedIntervalTreeMap[refName]) {
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
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  const intervalTree = new interval_tree_1.default();
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- (0, gtf_nostream_1.parseStringSync)(lines)
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+ for (const obj of (0, gtf_nostream_1.parseStringSync)(lines)
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  .flat()
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- .map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}`))
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- .forEach(obj => intervalTree.insert([obj.start, obj.end], obj));
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+ .map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}`))) {
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+ intervalTree.insert([obj.start, obj.end], obj);
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+ }
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  this.calculatedIntervalTreeMap[refName] = intervalTree;
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  }
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  return this.calculatedIntervalTreeMap[refName];
@@ -131,8 +132,8 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  await this.getFeaturesHelper({
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  query: {
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  ...query,
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- start: minStart,
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- end: maxEnd,
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+ start: minStart - 500000,
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+ end: maxEnd + 500000,
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  },
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  opts,
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  observer,
package/esm/GtfAdapter/GtfAdapter.js CHANGED
@@ -1,6 +1,6 @@
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  import IntervalTree from '@flatten-js/interval-tree';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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- import { SimpleFeature, doesIntersect2, fetchAndMaybeUnzip, max, min, } from '@jbrowse/core/util';
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+ import { SimpleFeature, doesIntersect2, fetchAndMaybeUnzip, getProgressDisplayStr, max, min, } from '@jbrowse/core/util';
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  import { openLocation } from '@jbrowse/core/util/io';
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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  import { parseStringSync } from 'gtf-nostream';
@@ -40,7 +40,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
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  }
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  }
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  if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
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+ statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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  }
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  blockStart = n + 1;
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  }
@@ -50,10 +50,11 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
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  if (!this.calculatedIntervalTreeMap[refName]) {
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
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  const intervalTree = new IntervalTree();
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- parseStringSync(lines)
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+ for (const obj of parseStringSync(lines)
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  .flat()
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- .map((f, i) => featureData(f, `${this.id}-${refName}-${i}`))
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- .forEach(obj => intervalTree.insert([obj.start, obj.end], obj));
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+ .map((f, i) => featureData(f, `${this.id}-${refName}-${i}`))) {
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+ intervalTree.insert([obj.start, obj.end], obj);
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+ }
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  this.calculatedIntervalTreeMap[refName] = intervalTree;
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  }
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  return this.calculatedIntervalTreeMap[refName];
@@ -126,8 +127,8 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
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  await this.getFeaturesHelper({
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  query: {
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  ...query,
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- start: minStart,
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- end: maxEnd,
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+ start: minStart - 500000,
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+ end: maxEnd + 500000,
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  },
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  opts,
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  observer,
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-gtf",
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- "version": "3.1.0",
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+ "version": "3.2.0",
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  "description": "JBrowse 2 gtf feature adapter",
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  "keywords": [
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  "jbrowse",
@@ -38,8 +38,8 @@
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  "dependencies": {
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  "@flatten-js/interval-tree": "^1.0.15",
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  "@gmod/bgzf-filehandle": "^2.0.1",
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- "@jbrowse/core": "^3.1.0",
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- "@jbrowse/plugin-linear-genome-view": "^3.1.0",
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+ "@jbrowse/core": "^3.2.0",
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+ "@jbrowse/plugin-linear-genome-view": "^3.2.0",
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  "@mui/material": "^6.0.0",
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  "gtf-nostream": "^1.0.0",
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  "mobx": "^6.0.0",
@@ -56,5 +56,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
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+ "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
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  }