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{ ParsedLocString, parseLocString } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nexport function bufferToString(buffer: Buffer) {\n  return new TextDecoder('utf8', { fatal: true }).decode(buffer)\n}\n\nasync function parseWith(buffer: Buffer, options = {}) {\n  const csv = await import('csvtojson').then(module => module.default)\n  return csv({ noheader: true, output: 'csv', ...options }).fromString(\n    bufferToString(buffer),\n  )\n}\n\nexport interface Row {\n  id: string\n\n  extendedData?: any\n  cells: {\n    text: string\n\n    extendedData?: any\n  }[]\n}\n\nexport interface RowSet {\n  isLoaded: boolean\n  rows: Row[]\n}\n\nexport interface ParseOptions {\n  hasColumnNameLine?: boolean\n  columnNameLineNumber?: number\n  selectedAssemblyName?: string\n  isValidRefName?: (refName: string, assemblyName?: string) => boolean\n}\n\nexport interface Column {\n  name: string\n  dataType: { type: string }\n  isDerived?: boolean\n  derivationFunctionText?: string\n}\n\nfunction guessColumnType(\n  rowSet: RowSet,\n  columnNumber: number,\n  isValidRefName: (refName: string, assemblyName?: string) => boolean,\n) {\n  const text = rowSet.rows[0]!.cells[columnNumber]!.text || ''\n\n  let guessedType = 'Text'\n\n  let parsedLoc: ParsedLocString | undefined\n  try {\n    parsedLoc = parseLocString(text, isValidRefName)\n  } catch (error) {\n    //\n  }\n  if (parsedLoc?.refName && typeof parsedLoc.start === 'number') {\n    guessedType = 'LocString'\n  } else if (/^\\d+(\\.\\d+)?$/.test(text)) {\n    guessedType = 'Number'\n  }\n\n  // MAYBE TODO: iterate over the rest of the rows to confirm\n  // the type for all the rows\n\n  return guessedType\n}\n\nfunction dataToSpreadsheetSnapshot(\n  rows: string[][],\n  options: ParseOptions = {},\n) {\n  const {\n    hasColumnNameLine = false,\n    columnNameLineNumber = 1,\n    isValidRefName = () => false,\n    selectedAssemblyName,\n  } = options\n  // rows is an array of row objects and columnNames\n  // is an array of column names (in import order)\n  let maxCols = 0\n  const rowSet: RowSet = {\n    isLoaded: true,\n    rows: rows.map((row, rowNumber) => {\n      const id = rowNumber + (hasColumnNameLine ? 0 : 1)\n      if (row.length > maxCols) {\n        maxCols = row.length\n      }\n      return {\n        id: String(id),\n        cells: row.map((text, columnNumber) => {\n          return { columnNumber, text }\n        }),\n      }\n    }),\n  }\n\n  // process the column names row if present\n  const columnNames: Record<string, string> = {}\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n  if (hasColumnNameLine && columnNameLineNumber !== undefined) {\n    const [colNamesRow] = rowSet.rows.splice(columnNameLineNumber - 1, 1)\n\n    if (colNamesRow) {\n      colNamesRow.cells.forEach((cell, columnNumber) => {\n        columnNames[columnNumber] = cell.text || ''\n      })\n    }\n  }\n\n  // make our column definitions\n  const columns: Column[] = []\n  const columnDisplayOrder = []\n  for (let columnNumber = 0; columnNumber < maxCols; columnNumber += 1) {\n    columnDisplayOrder.push(columnNumber)\n    const guessedType = guessColumnType(rowSet, columnNumber, isValidRefName)\n\n    // store extendeddata for LocString column\n    if (guessedType === 'LocString') {\n      for (const row of rowSet.rows) {\n        const cell = row.cells[columnNumber]!\n        cell.extendedData = parseLocString(cell.text, isValidRefName)\n      }\n    }\n\n    columns[columnNumber] = {\n      name: columnNames[columnNumber]!,\n      dataType: {\n        type: guessedType,\n      },\n    }\n  }\n\n  return {\n    rowSet,\n    columnDisplayOrder,\n    hasColumnNames: !!hasColumnNameLine,\n    columns,\n    assemblyName: selectedAssemblyName,\n  }\n}\n\nexport async function parseCsvBuffer(buffer: Buffer, options?: ParseOptions) {\n  const rows = await parseWith(buffer)\n  return dataToSpreadsheetSnapshot(rows, options)\n}\n\nexport async function parseTsvBuffer(buffer: Buffer, options?: ParseOptions) {\n  const rows = await parseWith(buffer, { delimiter: '\\t' })\n  return dataToSpreadsheetSnapshot(rows, options)\n}\n","import VCF from '@gmod/vcf'\nimport { VcfFeature } from '@jbrowse/plugin-variants'\nimport {\n  bufferToString,\n  Row,\n  RowSet,\n  Column,\n  ParseOptions,\n} from './ImportUtils'\nimport type { Buffer } from 'buffer'\n\nconst vcfCoreColumns: { name: string; type: string }[] = [\n  { name: 'CHROM', type: 'Text' }, // 0\n  { name: 'POS', type: 'Number' }, // 1\n  { name: 'ID', type: 'Text' }, // 2\n  { name: 'REF', type: 'Text' }, // 3\n  { name: 'ALT', type: 'Text' }, // 4\n  { name: 'QUAL', type: 'Number' }, // 5\n  { name: 'FILTER', type: 'Text' }, // 6\n  { name: 'INFO', type: 'Text' }, // 7\n  { name: 'FORMAT', type: 'Text' }, // 8\n]\n\nfunction vcfRecordToRow(vcfParser: any, line: string, lineNumber: number): Row {\n  const vcfVariant = vcfParser.parseLine(line)\n  const vcfFeature = new VcfFeature({\n    variant: vcfVariant,\n    parser: vcfParser,\n    id: `vcf-${lineNumber}`,\n  })\n\n  const data = line.split('\\t').map(d => (d === '.' ? '' : d))\n  // no format column, add blank\n  if (data.length === 8) {\n    data.push('')\n  }\n  const row: Row = {\n    id: String(lineNumber + 1),\n    extendedData: { vcfFeature: vcfFeature.toJSON() },\n    cells: data.map((text, columnNumber) => {\n      return {\n        columnNumber,\n        text,\n      }\n    }),\n  }\n  return row\n}\n\nexport function parseVcfBuffer(buffer: Buffer, options: ParseOptions = {}) {\n  const { selectedAssemblyName } = options\n  let { header, body } = splitVcfFileHeaderAndBody(bufferToString(buffer))\n  const rows: Row[] = []\n  const vcfParser = new VCF({ header })\n  header = '' // garbage collect\n  body.split(/\\n|\\r\\n|\\r/).forEach((line: string, lineNumber) => {\n    if (/\\S/.test(line)) {\n      rows.push(vcfRecordToRow(vcfParser, line, lineNumber))\n    }\n  })\n  body = '' // garbage collect\n\n  const rowSet: RowSet = {\n    isLoaded: true,\n    rows,\n  }\n\n  const columnDisplayOrder: number[] = []\n  const columns: Column[] = []\n  for (let i = 0; i < vcfCoreColumns.length; i += 1) {\n    columnDisplayOrder.push(i)\n    columns[i] = {\n      name: vcfCoreColumns[i]!.name,\n      dataType: { type: vcfCoreColumns[i]!.type },\n    }\n  }\n  for (let i = 0; i < vcfParser.samples.length; i += 1) {\n    const oi = vcfCoreColumns.length + i\n    columnDisplayOrder.push(oi)\n    columns[oi] = {\n      name: vcfParser.samples[i]!,\n      dataType: { type: 'Text' },\n    }\n  }\n\n  columnDisplayOrder.push(columnDisplayOrder.length)\n  columns.unshift({\n    name: 'Location',\n    dataType: { type: 'LocString' },\n    isDerived: true,\n    derivationFunctionText: `jexl:{text:row.extendedData.vcfFeature.refName+':'\\n\n    +row.extendedData.vcfFeature.start+'..'+row.extendedData.vcfFeature.end, extendedData:\\n\n    {refName:row.extendedData.vcfFeature.refName,start:row.extendedData.vcfFeature.start,end:row.extendedData.vcfFeature.end}}`,\n  })\n\n  return {\n    rowSet,\n    columnDisplayOrder,\n    hasColumnNames: true,\n    columns,\n    assemblyName: selectedAssemblyName,\n  }\n}\n\nexport function splitVcfFileHeaderAndBody(wholeFile: string) {\n  // split into header and the rest of the file\n  let headerEndIndex = 0\n  let prevChar: string | undefined\n  for (; headerEndIndex < wholeFile.length; headerEndIndex += 1) {\n    const c = wholeFile[headerEndIndex]\n    if (prevChar === '\\n' && c !== '#') {\n      break\n    }\n    prevChar = c\n  }\n\n  return {\n    header: wholeFile.slice(0, Math.max(0, headerEndIndex)),\n    body: wholeFile.slice(headerEndIndex),\n  }\n}\n"],"names":["bufferToString","buffer","TextDecoder","fatal","decode","async","parseWith","options","then","module","default","noheader","output","fromString","guessColumnType","rowSet","columnNumber","isValidRefName","text","rows","cells","parsedLoc","guessedType","parseLocString","error","refName","start","test","dataToSpreadsheetSnapshot","hasColumnNameLine","columnNameLineNumber","selectedAssemblyName","maxCols","isLoaded","map","row","rowNumber","id","length","String","columnNames","undefined","colNamesRow","splice","forEach","cell","columns","columnDisplayOrder","push","extendedData","name","dataType","type","hasColumnNames","assemblyName","parseCsvBuffer","parseTsvBuffer","delimiter","vcfCoreColumns","parseVcfBuffer","header","body","splitVcfFileHeaderAndBody","vcfParser","VCF","split","line","lineNumber","vcfVariant","parseLine","vcfFeature","VcfFeature","variant","parser","data","d","toJSON","vcfRecordToRow","i","samples","oi","unshift","isDerived","derivationFunctionText","wholeFile","prevChar","headerEndIndex","c","slice","Math","max"],"sourceRoot":""}