@jbrowse/plugin-gtf 3.6.3 → 3.6.5

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Files changed (3) hide show
  1. package/dist/GtfAdapter/GtfAdapter.js +16 -27
  2. package/esm/GtfAdapter/GtfAdapter.js +17 -28
  3. package/package.json +4 -4
package/dist/GtfAdapter/GtfAdapter.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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  const gtf_nostream_1 = require("gtf-nostream");
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  const util_2 = require("../util");
@@ -16,39 +17,27 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  this.calculatedIntervalTreeMap = {};
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  }
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  async loadDataP(opts) {
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- const { statusCallback = () => { } } = opts || {};
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  const loc = (0, io_1.openLocation)(this.getConf('gtfLocation'), this.pluginManager);
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  const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
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  const headerLines = [];
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  const featureMap = {};
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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 ret = line.indexOf('\t');
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- const refName = line.slice(0, ret);
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- if (!featureMap[refName]) {
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- featureMap[refName] = '';
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- }
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- featureMap[refName] += `${line}\n`;
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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 ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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+ else if (line.startsWith('>')) {
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+ return false;
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  }
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- blockStart = n + 1;
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- }
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+ else {
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+ const ret = line.indexOf('\t');
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+ const refName = line.slice(0, ret);
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+ if (!featureMap[refName]) {
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+ featureMap[refName] = '';
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+ }
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+ featureMap[refName] += `${line}\n`;
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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 intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
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  refName,
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  (sc) => {
package/esm/GtfAdapter/GtfAdapter.js CHANGED
@@ -1,7 +1,8 @@
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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, getProgressDisplayStr, max, min, } from '@jbrowse/core/util';
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+ import { SimpleFeature, doesIntersect2, fetchAndMaybeUnzip, max, min, } 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 { parseStringSync } from 'gtf-nostream';
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  import { featureData } from '../util';
@@ -11,39 +12,27 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
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  this.calculatedIntervalTreeMap = {};
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  }
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  async loadDataP(opts) {
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- const { statusCallback = () => { } } = opts || {};
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  const loc = openLocation(this.getConf('gtfLocation'), this.pluginManager);
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  const buffer = await fetchAndMaybeUnzip(loc, opts);
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  const headerLines = [];
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  const featureMap = {};
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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 ret = line.indexOf('\t');
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- const refName = line.slice(0, ret);
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- if (!featureMap[refName]) {
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- featureMap[refName] = '';
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- }
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- featureMap[refName] += `${line}\n`;
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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 ${getProgressDisplayStr(blockStart, buffer.length)}`);
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+ else if (line.startsWith('>')) {
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+ return false;
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  }
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- blockStart = n + 1;
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- }
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+ else {
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+ const ret = line.indexOf('\t');
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+ const refName = line.slice(0, ret);
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+ if (!featureMap[refName]) {
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+ featureMap[refName] = '';
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+ }
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+ featureMap[refName] += `${line}\n`;
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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 intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
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  refName,
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  (sc) => {
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": "3.6.3",
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+ "version": "3.6.5",
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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": "^4.0.0",
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- "@jbrowse/core": "^3.6.3",
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- "@jbrowse/plugin-linear-genome-view": "^3.6.3",
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+ "@jbrowse/core": "^3.6.5",
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+ "@jbrowse/plugin-linear-genome-view": "^3.6.5",
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  "@mui/material": "^7.0.0",
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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": "cf3dd1c895b4f3f7367093d57a0b607f54b8d7db"
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+ "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
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  }