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@module util */\n\n// Forks @gmod/gff-js and adapts it to parse and format GTF.\n\nconst fieldNames = [\n  'seq_name',\n  'source',\n  'featureType',\n  'start',\n  'end',\n  'score',\n  'strand',\n  'frame',\n  'attributes',\n]\n\n// TODO: check about enconding/escaping in gtf 9th column\n/**\n * Unescape a string/text value used in a GTF attribute.\n * Textual attributes should be surrounded by double quotes\n * source info:\n * https://mblab.wustl.edu/GTF22.html\n * https://en.wikipedia.org/wiki/Gene_transfer_format\n *\n * @param {String} s\n * @returns {String}\n */\nexport function unescape(s) {\n  if (s === null) {\n    return null\n  }\n  return String(s).replace(/%([0-9A-Fa-f]{2})/g, (_, seq) =>\n    String.fromCharCode(parseInt(seq, 16)),\n  )\n}\n\n/**\n * Escape a value for use in a GTF attribute value.\n *\n * @param {String} s\n * @returns {String}\n */\nfunction _escape(regex, s) {\n  return String(s).replace(regex, ch => {\n    let hex = ch.charCodeAt(0).toString(16).toUpperCase()\n\n    // lol, apparently there's no native function for fixed-width hex output\n    if (hex.length < 2) {\n      hex = `0${hex}`\n    }\n    return `%${hex}`\n  })\n}\n\nexport function escape(s) {\n  // eslint-disable-next-line no-control-regex\n  return _escape(/[\\n;\\r\\t=%&,\\x00-\\x1f\\x7f-\\xff]/g, s)\n}\n\n/**\n * Escape a value for use in a GTF column value.\n *\n * @param {String} s\n * @returns {String}\n */\nexport function escapeColumn(s) {\n  // eslint-disable-next-line no-control-regex\n  return _escape(/[\\n\\r\\t%\\x00-\\x1f\\x7f-\\xff]/g, s)\n}\n\n/**\n * Parse the 9th column (attributes) of a GTF feature line.\n *\n * @param {String} attrString\n * @returns {Object}\n */\nexport function parseAttributes(attrString) {\n  if (!(attrString && attrString.length) || attrString === '.') {\n    return {}\n  }\n\n  const attrs = {}\n\n  attrString\n    .replace(/\\r?\\n$/, '')\n    .slice(0, -1) // need to remove the last semicolon in the attributes\n    .split(';')\n    .forEach(attribute => {\n      if (!attribute) {\n        return\n      }\n      const attr = attribute.trim().split(' ')\n      if (!(attr[1] && attr[1].length)) {\n        return\n      }\n\n      attr[0] = attr[0].trim()\n      let arec = attrs[attr[0].trim()]\n      if (!arec) {\n        arec = []\n        attrs[attr[0]] = arec\n      }\n\n      // arec.push(unescape(attr[1].trim()))\n      arec.push(\n        ...attr[1]\n          .split(',')\n          .map(s => s.trim())\n          .map(unescape),\n      )\n    })\n  return attrs\n}\n\n/**\n * Parse a GTF feature line.\n *\n * @param {String} line\n * returns the parsed line in an object\n */\nexport function parseFeature(line) {\n  // assumed that there are no comments at the end of a line\n  // split the line into columns and replace '.' with null in each column\n  const f = line.split('\\t').map(a => (a === '.' ? null : a))\n\n  // unescape only the seq_name, source, and feature columns\n  f[0] = unescape(f[0])\n  f[1] = unescape(f[1])\n  f[2] = unescape(f[2])\n\n  f[8] = parseAttributes(f[8])\n  const parsed = {}\n  for (let i = 0; i < fieldNames.length; i += 1) {\n    parsed[fieldNames[i]] = f[i] === '.' ? null : f[i]\n  }\n  if (parsed.start !== null) {\n    parsed.start = parseInt(parsed.start, 10)\n  }\n  if (parsed.end !== null) {\n    parsed.end = parseInt(parsed.end, 10)\n  }\n  if (parsed.score !== null) {\n    parsed.score = parseFloat(parsed.score, 10)\n  }\n  if (parsed.strand != null) {\n    parsed.strand = parsed.strand\n  }\n  return parsed\n}\n\n/**\n * Parse a GTF directive/comment line.\n *\n * @param {String} line\n * @returns {Object} the information in the directive\n */\nexport function parseDirective(line) {\n  const match = /^\\s*##\\s*(\\S+)\\s*(.*)/.exec(line)\n  // const match = /^\\s*\\#\\#\\s*(\\S+)\\s*(.*)/.exec(line)\n  if (!match) {\n    return null\n  }\n\n  // let [, name, contents] = match\n  const name = match[1]\n  let contents = match[2]\n  const parsed = { directive: name }\n  if (contents.length) {\n    contents = contents.replace(/\\r?\\n$/, '')\n    parsed.value = contents\n  }\n\n  // do a little additional parsing for sequence-region and genome-build directives\n  if (name === 'sequence-region') {\n    const [seqId, contentStart, contentEnd] = contents.split(/\\s+/, 3)\n    parsed.seq_id = seqId\n    parsed.start = contentStart && contentStart.replace(/\\D/g, '')\n    parsed.end = contentEnd && contentEnd.replace(/\\D/g, '')\n  } else if (name === 'genome-build') {\n    const [source, buildname] = contents.split(/\\s+/, 2)\n    parsed.source = source\n    parsed.buildname = buildname\n  }\n\n  return parsed\n}\n\n/**\n * Format an attributes object into a string suitable for the 9th column of GTF.\n *\n * @param {Object} attrs\n */\nexport function formatAttributes(attrs) {\n  const attrOrder = []\n  Object.keys(attrs).forEach(tag => {\n    const val = attrs[tag]\n    let valstring\n    // eslint-disable-next-line no-prototype-builtins\n    if (val.hasOwnProperty('toString')) {\n      valstring = escape(val.toString())\n    } else if (Array.isArray(val.values)) {\n      valstring = val.values.map(escape).join(',')\n    } else if (Array.isArray(val)) {\n      valstring = val.map(escape).join(',')\n    } else {\n      valstring = escape(val)\n    }\n    attrOrder.push(`${escape(tag)} ${valstring}`)\n  })\n  return attrOrder.length ? attrOrder.join('; ').concat(';') : '.'\n}\n\nconst translateStrand = ['-', '.', '+']\n\nfunction _formatSingleFeature(f, seenFeature) {\n  const attrString =\n    f.attributes === null || f.attributes === undefined\n      ? '.'\n      : formatAttributes(f.attributes)\n\n  const fields = []\n  for (let i = 0; i < 8; i += 1) {\n    const val = f[fieldNames[i]]\n    // deserialize strand\n    if (i === 6) {\n      fields[i] =\n        val === null || val === undefined\n          ? '.'\n          : translateStrand[val + 1] || val\n    } else {\n      fields[i] =\n        val === null || val === undefined ? '.' : escapeColumn(String(val))\n    }\n  }\n  fields[8] = attrString\n\n  const formattedString = `${fields.join('\\t')}\\n`\n\n  // if we have already output this exact feature, skip it\n  if (seenFeature[formattedString]) {\n    return ''\n  }\n\n  // eslint-disable-next-line no-param-reassign\n  seenFeature[formattedString] = true\n  return formattedString\n}\n\nfunction _formatFeature(feature, seenFeature) {\n  if (Array.isArray(feature)) {\n    return feature.map(f => _formatFeature(f, seenFeature)).join('')\n  }\n\n  const strings = [_formatSingleFeature(feature, seenFeature)]\n  ;['child_features', 'derived_features'].forEach(multiSlot => {\n    if (feature[multiSlot]) {\n      strings.push(\n        ...feature[multiSlot].map(f => _formatFeature(f, seenFeature)),\n      )\n    }\n  })\n  return strings.join('')\n}\n\n/**\n * Format a feature object or array of\n * feature objects into one or more lines of GTF.\n *\n * @param {Object|Array[Object]} featureOrFeatures\n */\nexport function formatFeature(featureOrFeatures) {\n  const seen = {}\n  return _formatFeature(featureOrFeatures, seen)\n}\n\n/**\n * Format a directive into a line of GTF.\n *\n * @param {Object} directive\n * @returns {String}\n */\nexport function formatDirective(directive) {\n  let str = `##${directive.directive}`\n  if (directive.value) {\n    str += ` ${directive.value}`\n  }\n  str += '\\n'\n  return str\n}\n\n/**\n * Format a comment into a GTF comment.\n * Yes I know this is just adding a # and a newline.\n *\n * @param {Object} comment\n * @returns {String}\n */\nexport function formatComment(comment) {\n  return `# ${comment.comment}\\n`\n}\n\n/**\n * Format a sequence object as FASTA\n *\n * @param {Object} seq\n * @returns {String} formatted single FASTA sequence\n */\nexport function formatSequence(seq) {\n  return `>${seq.id}${seq.description ? ` ${seq.description}` : ''}\\n${\n    seq.sequence\n  }\\n`\n}\n\n/**\n * Format a directive, comment, or feature,\n * or array of such items, into one or more lines of GTF.\n *\n * @param {Object|Array} itemOrItems\n */\nexport function formatItem(itemOrItems) {\n  function formatSingleItem(item) {\n    if (item[0] || item.attributes) {\n      return formatFeature(item)\n    }\n    if (item.directive) {\n      return formatDirective(item)\n    }\n    if (item.sequence) {\n      return formatSequence(item)\n    }\n    if (item.comment) {\n      return formatComment(item)\n    }\n    return '# (invalid item found during format)\\n'\n  }\n\n  if (Array.isArray(itemOrItems)) {\n    return itemOrItems.map(item => formatSingleItem(item))\n  }\n  return formatSingleItem(itemOrItems)\n}\n","//@ts-nocheck\nimport * as GTF from './util'\n\nconst containerAttributes = {\n  Parent: 'child_features',\n  Derives_from: 'derived_features',\n}\n\nexport default class Parser {\n  constructor(args) {\n    // eslint-disable-next-line @typescript-eslint/no-empty-function\n    const nullFunc = () => {}\n\n    Object.assign(this, {\n      featureCallback: args.featureCallback || nullFunc,\n      endCallback: args.endCallback || nullFunc,\n      commentCallback: args.commentCallback || nullFunc,\n      errorCallback: args.errorCallback || nullFunc,\n      directiveCallback: args.directiveCallback || nullFunc,\n      sequenceCallback: args.sequenceCallback || nullFunc,\n\n      // number of lines to buffer\n      bufferSize: args.bufferSize === undefined ? 1000 : args.bufferSize,\n\n      // features that we have to keep on hand for now because they\n      // might be referenced by something else\n      _underConstructionTopLevel: [],\n      // index of the above by ID\n      _underConstructionById: {},\n\n      _completedReferences: {},\n\n      // features that reference something we have not seen yet\n      // structured as:\n      // {  'some_id' : {\n      //     'Parent' : [ orphans that have a Parent attr referencing it ],\n      //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],\n      //    }\n      // }\n      _underConstructionOrphans: {},\n\n      // if this is true, the parser ignores the\n      // rest of the lines in the file.\n      eof: false,\n\n      lineNumber: 0,\n    })\n  }\n\n  addLine(line) {\n    if (this.eof) {\n      // otherwise, if we are done, ignore this line\n      return\n    }\n\n    this.lineNumber += 1\n\n    if (/^\\s*[^#\\s>]/.test(line)) {\n      // feature line, most common case\n      this._bufferLine(line)\n      return\n    }\n\n    const match = /^\\s*(#+)(.*)/.exec(line)\n    if (match) {\n      // directive or comment\n      // eslint-disable-next-line prefer-const\n      let [, hashsigns, contents] = match\n\n      if (hashsigns.length === 3) {\n        // sync directive, all forward-references are resolved.\n        this._emitAllUnderConstructionFeatures()\n      } else if (hashsigns.length === 2) {\n        const directive = GTF.parseDirective(line)\n\n        this._emitItem(directive)\n      } else {\n        contents = contents.replace(/\\s*/, '')\n        this._emitItem({ comment: contents })\n      }\n    } else if (/^\\s*$/.test(line)) {\n      // blank line, do nothing\n    } else {\n      // it's a parse error\n      const errLine = line.replace(/\\r?\\n?$/g, '')\n      throw new Error(`GTF parse error.  Cannot parse '${errLine}'.`)\n    }\n  }\n\n  _emitItem(i) {\n    if (i[0]) {\n      this.featureCallback(i)\n    } else if (i.directive) {\n      this.directiveCallback(i)\n    } else if (i.comment) {\n      this.commentCallback(i)\n    }\n  }\n\n  finish() {\n    this._emitAllUnderConstructionFeatures()\n    this.endCallback()\n  }\n\n  _enforceBufferSizeLimit(additionalItemCount = 0) {\n    const _unbufferItem = item => {\n      if (\n        item?.[0]?.attributes?.ID?.[0]\n      ) {\n        const ids = item[0].attributes.ID\n        ids.forEach(id => {\n          delete this._underConstructionById[id]\n          delete this._completedReferences[id]\n        })\n        item.forEach(i => {\n          if (i.child_features) {\n            i.child_features.forEach(c => { _unbufferItem(c) })\n          }\n          if (i.derived_features) {\n            i.derived_features.forEach(d => { _unbufferItem(d) })\n          }\n        })\n      }\n    }\n\n    while (\n      this._underConstructionTopLevel.length + additionalItemCount >\n      this.bufferSize\n    ) {\n      const item = this._underConstructionTopLevel.shift()\n      this._emitItem(item)\n      _unbufferItem(item)\n    }\n  }\n\n  /**\n   * return all under-construction features, called when we know\n   * there will be no additional data to attach to them\n   * @private\n   */\n  _emitAllUnderConstructionFeatures() {\n    this._underConstructionTopLevel.forEach(this._emitItem.bind(this))\n\n    this._underConstructionTopLevel = []\n    this._underConstructionById = {}\n    this._completedReferences = {}\n\n    // if we have any orphans hanging around still, this is a\n    // problem. die with a parse error\n    if (\n      Object.values(this._underConstructionOrphans).filter(\n        entry => Object.keys(entry).length,\n      ).length\n    ) {\n      throw new Error(\n        `some features reference other features that do not exist in the file (or in the same '###' scope). ${JSON.stringify(\n          this._underConstructionOrphans,\n        )}`,\n      )\n    }\n  }\n\n  // do the right thing with a newly-parsed feature line\n  _bufferLine(line) {\n    const featureLine = GTF.parseFeature(line)\n    featureLine.child_features = []\n    featureLine.derived_features = []\n    // featureLine._lineNumber = this.lineNumber //< debugging aid\n\n    const featureNumber = this.lineNumber // no such thing as unique ID in GTF. make one up.\n    const isTranscript = featureLine.featureType === 'transcript' // trying to support the Cufflinks convention of adding a transcript line\n    // NOTE: a feature is an arrayref of one or more feature lines.\n    const ids = isTranscript\n      ? featureLine.attributes.transcript_id || []\n      : [featureNumber]\n    const parents = isTranscript\n      ? []\n      : featureLine.attributes.transcript_id || []\n    const derives = featureLine.attributes.Derives_from || []\n\n    if (!ids.length && !parents.length && !derives.length) {\n      // if it has no IDs and does not refer to anything, we can just\n      // output it\n      this._emitItem([featureLine])\n      return\n    }\n\n    function createTranscript(feature) {\n      const result = JSON.parse(JSON.stringify(feature))\n      result.featureType = 'transcript'\n      return GTF.formatFeature(result)\n    }\n\n    parents.forEach(parent => {\n      const underConst = this._underConstructionById[parent]\n      if (!underConst) {\n        this._bufferLine(createTranscript(featureLine))\n      }\n    })\n\n    let feature\n    ids.forEach(id => {\n      const existing = this._underConstructionById[id]\n      if (existing) {\n        existing.push(featureLine)\n        feature = existing\n      } else {\n        // haven't seen it yet, so buffer it so we can attach\n        // child features to it\n        feature = [featureLine]\n\n        this._enforceBufferSizeLimit(1)\n        if (!parents.length && !derives.length) {\n          this._underConstructionTopLevel.push(feature)\n        }\n        this._underConstructionById[id] = feature\n\n        // see if we have anything buffered that refers to it\n        this._resolveReferencesTo(feature, id)\n      }\n    })\n\n    // try to resolve all its references\n    this._resolveReferencesFrom(\n      feature || [featureLine],\n      { Parent: parents, Derives_from: derives },\n      ids,\n    )\n  }\n\n  _resolveReferencesTo(feature, id) {\n    const references = this._underConstructionOrphans[id]\n    if (!references) {\n      return\n    }\n\n    Object.keys(references).forEach(attrname => {\n      const pname = containerAttributes[attrname] || attrname.toLowerCase()\n      feature.forEach(loc => {\n        loc[pname].push(...references[attrname])\n        delete references[attrname]\n      })\n    })\n  }\n\n  _parseError(message) {\n    this.eof = true\n    this.errorCallback(`${this.lineNumber}: ${message}`)\n  }\n\n  _resolveReferencesFrom(feature, references, ids) {\n    // this is all a bit more awkward in javascript than it was in perl\n    function postSet(obj, slot1, slot2) {\n      let subObj = obj[slot1]\n      if (!subObj) {\n        subObj = {}\n         \n        obj[slot1] = subObj\n      }\n      const returnVal = subObj[slot2] || false\n      subObj[slot2] = true\n      return returnVal\n    }\n\n    function expandFeature(parentFeature, childFeature) {\n       \n      parentFeature[0].start = Math.min(\n        parentFeature[0].start,\n        childFeature[0].start,\n      )\n       \n      parentFeature[0].end = Math.max(parentFeature[0].end, childFeature[0].end)\n    }\n\n    Object.entries(references).forEach(([attrname, toIds]) => {\n      let pname\n      toIds.forEach(toId => {\n        const otherFeature = this._underConstructionById[toId]\n        if (otherFeature) {\n          expandFeature(otherFeature, feature)\n          if (!pname) {\n            pname = containerAttributes[attrname] || attrname.toLowerCase()\n          }\n\n          if (\n            !ids.filter(id =>\n              postSet(this._completedReferences, id, `${attrname},${toId}`),\n            ).length\n          ) {\n            otherFeature.forEach(location => {\n              location[pname].push(feature)\n            })\n          }\n        } else {\n          if (!this._underConstructionOrphans[toId]) {\n            this._underConstructionOrphans[toId] = {}\n          }\n          if (!this._underConstructionOrphans[toId][attrname]) {\n            this._underConstructionOrphans[toId][attrname] = []\n          }\n          this._underConstructionOrphans[toId][attrname].push(feature)\n        }\n      })\n    })\n  }\n}\n","export type Strand = '+' | '-' | '.' | '?'\nexport interface FeatureLoc {\n  [key: string]: unknown\n  start: number\n  end: number\n  strand: Strand\n  seq_name: string\n  child_features?: FeatureLoc[][]\n  data: unknown\n  derived_features: unknown\n  attributes: Record<string, unknown[]>\n}\n\nexport function featureData(data: FeatureLoc) {\n  const f: Record<string, unknown> = { ...data }\n  ;(f.start as number) -= 1 // convert to interbase\n  f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand] // convert strand\n  f.phase = Number(data.frame)\n  f.refName = data.seq_name\n  if (data.score === null) {\n    f.score = undefined\n  }\n  if (data.frame === null) {\n    f.score = undefined\n  }\n  const defaultFields = new Set([\n    'start',\n    'end',\n    'seq_name',\n    'score',\n    'featureType',\n    'source',\n    'frame',\n    'strand',\n  ])\n  for (const a of Object.keys(data.attributes)) {\n    let b = a.toLowerCase()\n    if (defaultFields.has(b)) {\n      // add \"suffix\" to tag name if it already exists\n      // reproduces behavior of NCList\n      b += '2'\n    }\n    if (data.attributes[a]) {\n      let attr = data.attributes[a] as string[] | string\n      if (Array.isArray(attr) && attr.length === 1) {\n        // gtf uses double quotes for text values in the attributes column,\n        // remove them\n        attr = attr[0]!.replaceAll(/^\"|\"$/g, '')\n      }\n      f[b] = attr\n    }\n  }\n  f.refName = f.seq_name\n  f.type = f.featureType\n\n  // the SimpleFeature constructor takes care of recursively inflating subfeatures\n  if (data.child_features && data.child_features.length > 0) {\n    f.subfeatures = data.child_features.flatMap(childLocs =>\n      childLocs.map(childLoc => featureData(childLoc)),\n    )\n  }\n\n  f.child_features = undefined\n  f.data = undefined\n  f.derived_features = undefined\n  f._linehash = undefined\n  f.attributes = undefined\n  f.seq_name = undefined\n  f.featureType = undefined\n  f.frame = undefined\n\n  if (f.transcript_id) {\n    f.name = f.transcript_id\n  }\n  return f\n}\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport {\n  SimpleFeature,\n  Feature,\n  updateStatus,\n  isGzip,\n} from '@jbrowse/core/util'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { parseStringSync } from 'gtf-nostream'\nimport type { Buffer } from 'buffer'\n\n// locals\nimport { FeatureLoc, featureData } from '../util'\n\nconst decoder =\n  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\ntype StatusCallback = (arg: string) => void\n\nexport default class GtfAdapter extends BaseFeatureDataAdapter {\n  calculatedIntervalTreeMap: Record<string, IntervalTree> = {}\n\n  gtfFeatures?: Promise<{\n    header: string\n    intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>\n  }>\n\n  private async loadDataP(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    const buf = (await openLocation(\n      this.getConf('gtfLocation'),\n      this.pluginManager,\n    ).readFile(opts)) as Buffer\n\n    const buffer = isGzip(buf)\n      ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))\n      : buf\n    const headerLines = []\n    const featureMap = {} as Record<string, string>\n    let blockStart = 0\n\n    let i = 0\n    while (blockStart < buffer.length) {\n      const n = buffer.indexOf('\\n', blockStart)\n      // could be a non-newline ended file, so slice to end of file if n===-1\n      const b =\n        n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n)\n      const line = (decoder?.decode(b) || b.toString()).trim()\n      if (line) {\n        if (line.startsWith('#')) {\n          headerLines.push(line)\n        } else if (line.startsWith('>')) {\n          break\n        } else {\n          const ret = line.indexOf('\\t')\n          const refName = line.slice(0, ret)\n          if (!featureMap[refName]) {\n            featureMap[refName] = ''\n          }\n          featureMap[refName] += `${line}\\n`\n        }\n      }\n      if (i++ % 10_000 === 0) {\n        statusCallback(\n          `Loading ${Math.floor(blockStart / 1_000_000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1_000_000).toLocaleString('en-US')} MB`,\n        )\n      }\n\n      blockStart = n + 1\n    }\n\n    const intervalTreeMap = Object.fromEntries(\n      Object.entries(featureMap).map(([refName, lines]) => [\n        refName,\n        (sc?: (arg: string) => void) => {\n          if (!this.calculatedIntervalTreeMap[refName]) {\n            sc?.('Parsing GTF data')\n            const intervalTree = new IntervalTree()\n            ;(parseStringSync(lines) as FeatureLoc[][])\n              .flat()\n              .map(\n                (f, i) =>\n                  new SimpleFeature({\n                    data: featureData(f),\n                    id: `${this.id}-${refName}-${i}`,\n                  }),\n              )\n              .forEach(obj =>\n                intervalTree.insert([obj.get('start'), obj.get('end')], obj),\n              )\n            this.calculatedIntervalTreeMap[refName] = intervalTree\n          }\n          return this.calculatedIntervalTreeMap[refName]\n        },\n      ]),\n    )\n\n    return {\n      header: headerLines.join('\\n'),\n      intervalTreeMap,\n    }\n  }\n\n  private async loadData(opts: BaseOptions = {}) {\n    if (!this.gtfFeatures) {\n      this.gtfFeatures = this.loadDataP(opts).catch((e: unknown) => {\n        this.gtfFeatures = undefined\n        throw e\n      })\n    }\n\n    return this.gtfFeatures\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    const { intervalTreeMap } = await this.loadData(opts)\n    return Object.keys(intervalTreeMap)\n  }\n\n  public async getHeader(opts: BaseOptions = {}) {\n    const { header } = await this.loadData(opts)\n    return header\n  }\n\n  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      try {\n        const { start, end, refName } = query\n        const { intervalTreeMap } = await this.loadData(opts)\n        intervalTreeMap[refName]?.(opts.statusCallback)\n          .search([start, end])\n          .forEach(f => {\n            observer.next(f)\n          })\n        observer.complete()\n      } catch (e) {\n        observer.error(e)\n      }\n    }, opts.signal)\n  }\n  public freeResources(/* { region } */) {}\n}\n","import Parser from './parse'\n\nexport function parseStringSync(str: string): unknown[] {\n  if (!str) {\n    return []\n  }\n\n  const items: unknown[] = []\n\n  const parser = new Parser({\n    // @ts-expect-error\n    featureCallback: item => items.push(item),\n    // @ts-expect-error\n    errorCallback: err => {\n      throw err\n    },\n  })\n\n  for (const line of str.split(/\\r?\\n/)) {\n    parser.addLine(line)\n  }\n  parser.finish()\n\n  return 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