const {TabixIndexedFile} = require('@gmod/tabix')

const tbiIndexed = new TabixIndexedFile({ path: 'path/to/my/file.gz' })
// by default, assumes tabix index at path/to/my/file.gz.tbi.
// can also provide `tbiPath` if the TBI is named differently

// can also open tabix files that have a .csi index
const csiIndexed = new TabixIndexedFile({
  path: 'path/to/my/file.gz',
  csiPath: 'path/to/my/file.gz.csi'
})

// use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle
const {RemoteFile} = require('generic-filehandle')
const remoteTbiIndexed = new TabixIndexedFile({
  filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi') // can also be csiFilehandle
})

// iterate over lines in the specified region
const lines = []
await tbiIndexed.getLines('ctgA',200,300, (line, fileOffset) => lines.push(line))
// alternative API usage
const aborter = new AbortController()
await tbiIndexed.getLines('ctgA',200,300, {
  lineCallback: (line, fileOffset) => lines.push(line),
  signal: aborter.signal // an optional AbortSignal from an AbortController
})
// lines is now an array of strings, which are data lines.
// commented (meta) lines are skipped.
// line strings do not include any trailing whitespace characters.
// the callback is also called with a `fileOffset`,
// which gives the virtual file offset where the line is found in the file

// get the approximate number of data lines in the
// file for the given reference sequence, excluding header, comment, and whitespace lines
const numLines = await tbiIndexed.lineCount('ctgA')
// or const numLines = await tbiIndexed.lineCount('ctgA', { signal: aborter.signal })

// get the "header text" string from the file, which is the first contiguous
// set of lines in the file that all start with a "meta" character (usually #)
const headerText = await tbiIndexed.getHeader()
// or const headerText = await tbiIndexed.getHeader({ signal: aborter.signal })

// or if you want a nodejs Buffer object instead, there is getHeaderBuffer()
const headerBuffer = await tbiIndexed.getHeaderBuffer()
// or const headerBuffer = await tbiIndexed.getHeaderBuffer({ signal: aborter.signal })