@jbrowse/plugin-bed 3.6.3 → 3.6.5

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Files changed (7) hide show
  1. package/dist/BedAdapter/BedAdapter.js +13 -27
  2. package/dist/BedGraphAdapter/BedGraphAdapter.js +16 -20
  3. package/dist/BigBedAdapter/BigBedAdapter.js +1 -4
  4. package/esm/BedAdapter/BedAdapter.js +14 -28
  5. package/esm/BedGraphAdapter/BedGraphAdapter.js +16 -20
  6. package/esm/BigBedAdapter/BigBedAdapter.js +1 -4
  7. package/package.json +3 -3
package/dist/BedAdapter/BedAdapter.js CHANGED
@@ -8,6 +8,7 @@ const bed_1 = __importDefault(require("@gmod/bed"));
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  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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  const util_1 = require("@jbrowse/core/util");
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  const io_1 = require("@jbrowse/core/util/io");
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+ const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
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  const rxjs_1 = require("@jbrowse/core/util/rxjs");
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  const util_2 = require("../util");
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  class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -16,39 +17,24 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  this.intervalTrees = {};
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  }
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  async loadDataP(opts) {
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- const { statusCallback = () => { } } = opts || {};
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  const bedLoc = this.getConf('bedLocation');
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  const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, this.pluginManager), opts);
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  const headerLines = [];
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  const features = {};
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- let blockStart = 0;
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- let i = 0;
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- const decoder = new TextDecoder('utf8');
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- while (blockStart < buffer.length) {
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- const n = buffer.indexOf(10, blockStart);
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- const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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- const line = decoder.decode(b).trim();
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- if (line) {
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- if (line.startsWith('#')) {
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- headerLines.push(line);
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- }
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- else if (line.startsWith('>')) {
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- break;
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- }
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- else {
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- const tab = line.indexOf('\t');
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- const refName = line.slice(0, tab);
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- if (!features[refName]) {
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- features[refName] = [];
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- }
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- features[refName].push(line);
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- }
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+ (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
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+ if (line.startsWith('#')) {
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+ headerLines.push(line);
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  }
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- if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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+ else {
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+ const tab = line.indexOf('\t');
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+ const refName = line.slice(0, tab);
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+ if (!features[refName]) {
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+ features[refName] = [];
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+ }
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+ features[refName].push(line);
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  }
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- blockStart = n + 1;
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- }
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+ return true;
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+ }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
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  const header = headerLines.join('\n');
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  const autoSql = this.getConf('autoSql');
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  const parser = new bed_1.default({ autoSql });
package/dist/BedGraphAdapter/BedGraphAdapter.js CHANGED
@@ -7,6 +7,7 @@ const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
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  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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  const util_1 = require("@jbrowse/core/util");
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  const io_1 = require("@jbrowse/core/util/io");
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+ const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
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  const rxjs_1 = require("@jbrowse/core/util/rxjs");
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  class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  constructor() {
@@ -69,30 +70,25 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  const pm = this.pluginManager;
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  const bedLoc = this.getConf('bedGraphLocation');
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  const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
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- if (buffer.length > 536870888) {
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- throw new Error('Data exceeds maximum string length (512MB)');
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- }
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- const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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- const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
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- const headerLines = [];
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- let i = 0;
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- for (; i < lines.length && lines[i].startsWith('#'); i++) {
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- headerLines.push(lines[i]);
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- }
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- const header = headerLines.join('\n');
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  const features = {};
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- for (; i < lines.length; i++) {
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- const line = lines[i];
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- const tab = line.indexOf('\t');
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- const refName = line.slice(0, tab);
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- if (!features[refName]) {
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- features[refName] = [];
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+ const headerLines = [];
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+ (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
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+ if (line.startsWith('#')) {
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+ headerLines.push(line);
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  }
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- features[refName].push(line);
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- }
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+ else {
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+ const tab = line.indexOf('\t');
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+ const refName = line.slice(0, tab);
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+ if (!features[refName]) {
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+ features[refName] = [];
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+ }
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+ features[refName].push(line);
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+ }
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+ return true;
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+ }, opts.statusCallback);
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  const columnNames = this.getConf('columnNames');
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  return {
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- header,
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+ header: headerLines.join('\n'),
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  features,
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  columnNames,
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  };
package/dist/BigBedAdapter/BigBedAdapter.js CHANGED
@@ -172,10 +172,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  const e = (0, util_1.max)(subfeatures.map(f => f.end));
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  if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
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  const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
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- if (subs.every(s => {
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- var _a;
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- return s.strand === (((_a = subs[0]) === null || _a === void 0 ? void 0 : _a.strand) || 1);
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- })) {
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+ if (subs.some((a, i) => subs.some((b, j) => i !== j && (0, util_1.doesIntersect2)(a.start, a.end, b.start, b.end)))) {
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  observer.next(new util_1.SimpleFeature({
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  id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
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  data: {
package/esm/BedAdapter/BedAdapter.js CHANGED
@@ -1,8 +1,9 @@
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  import IntervalTree from '@flatten-js/interval-tree';
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  import BED from '@gmod/bed';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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- import { SimpleFeature, fetchAndMaybeUnzip, getProgressDisplayStr, } from '@jbrowse/core/util';
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+ import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
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  import { openLocation } from '@jbrowse/core/util/io';
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+ import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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  import { featureData } from '../util';
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  class BedAdapter extends BaseFeatureDataAdapter {
@@ -11,39 +12,24 @@ class BedAdapter extends BaseFeatureDataAdapter {
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  this.intervalTrees = {};
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  }
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  async loadDataP(opts) {
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- const { statusCallback = () => { } } = opts || {};
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  const bedLoc = this.getConf('bedLocation');
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  const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, this.pluginManager), opts);
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  const headerLines = [];
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  const features = {};
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- let blockStart = 0;
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- let i = 0;
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- const decoder = new TextDecoder('utf8');
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- while (blockStart < buffer.length) {
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- const n = buffer.indexOf(10, blockStart);
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- const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
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- const line = decoder.decode(b).trim();
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- if (line) {
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- if (line.startsWith('#')) {
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- headerLines.push(line);
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- }
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- else if (line.startsWith('>')) {
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- break;
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- }
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- else {
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- const tab = line.indexOf('\t');
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- const refName = line.slice(0, tab);
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- if (!features[refName]) {
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- features[refName] = [];
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- }
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- features[refName].push(line);
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- }
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+ parseLineByLine(buffer, line => {
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+ if (line.startsWith('#')) {
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+ headerLines.push(line);
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  }
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- if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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+ else {
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+ const tab = line.indexOf('\t');
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+ const refName = line.slice(0, tab);
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+ if (!features[refName]) {
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+ features[refName] = [];
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+ }
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+ features[refName].push(line);
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  }
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- blockStart = n + 1;
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- }
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+ return true;
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+ }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
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  const header = headerLines.join('\n');
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  const autoSql = this.getConf('autoSql');
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  const parser = new BED({ autoSql });
package/esm/BedGraphAdapter/BedGraphAdapter.js CHANGED
@@ -2,6 +2,7 @@ import IntervalTree from '@flatten-js/interval-tree';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
3
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  import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
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  import { openLocation } from '@jbrowse/core/util/io';
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+ import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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  export default class BedGraphAdapter extends BaseFeatureDataAdapter {
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  constructor() {
@@ -64,30 +65,25 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
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  const pm = this.pluginManager;
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  const bedLoc = this.getConf('bedGraphLocation');
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  const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
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- if (buffer.length > 536870888) {
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- throw new Error('Data exceeds maximum string length (512MB)');
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- }
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- const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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- const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
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- const headerLines = [];
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- let i = 0;
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- for (; i < lines.length && lines[i].startsWith('#'); i++) {
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- headerLines.push(lines[i]);
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- }
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- const header = headerLines.join('\n');
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  const features = {};
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- for (; i < lines.length; i++) {
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- const line = lines[i];
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- const tab = line.indexOf('\t');
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- const refName = line.slice(0, tab);
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- if (!features[refName]) {
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- features[refName] = [];
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+ const headerLines = [];
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+ parseLineByLine(buffer, line => {
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+ if (line.startsWith('#')) {
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+ headerLines.push(line);
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  }
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- features[refName].push(line);
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- }
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+ else {
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+ const tab = line.indexOf('\t');
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+ const refName = line.slice(0, tab);
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+ if (!features[refName]) {
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+ features[refName] = [];
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+ }
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+ features[refName].push(line);
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+ }
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+ return true;
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+ }, opts.statusCallback);
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  const columnNames = this.getConf('columnNames');
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  return {
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- header,
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+ header: headerLines.join('\n'),
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  features,
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  columnNames,
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  };
package/esm/BigBedAdapter/BigBedAdapter.js CHANGED
@@ -167,10 +167,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
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  const e = max(subfeatures.map(f => f.end));
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  if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
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  const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
170
- if (subs.every(s => {
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- var _a;
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- return s.strand === (((_a = subs[0]) === null || _a === void 0 ? void 0 : _a.strand) || 1);
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- })) {
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+ if (subs.some((a, i) => subs.some((b, j) => i !== j && doesIntersect2(a.start, a.end, b.start, b.end)))) {
174
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  observer.next(new SimpleFeature({
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  id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
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  data: {
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-bed",
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- "version": "3.6.3",
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+ "version": "3.6.5",
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  "description": "JBrowse 2 bed adapters, tracks, etc.",
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  "keywords": [
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  "jbrowse",
@@ -41,7 +41,7 @@
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  "@gmod/bed": "^2.1.2",
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  "@gmod/bgzf-filehandle": "^4.0.0",
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  "@gmod/tabix": "^3.0.1",
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- "@jbrowse/core": "^3.6.3",
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+ "@jbrowse/core": "^3.6.5",
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  "mobx": "^6.0.0",
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  "mobx-react": "^9.0.0",
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  "mobx-state-tree": "^5.0.0",
@@ -53,5 +53,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
56
- "gitHead": "cf3dd1c895b4f3f7367093d57a0b607f54b8d7db"
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+ "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
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  }