nclist-js

Read legacy JBrowse 1 nested containment list JSON.

Status

Usage

import { RemoteFile } from 'generic-filehandle2'
import NCList from '@gmod/nclist'
;(async () => {
  const store = new NCList({
    baseUrl: `http://my.server/path/to/data/dir/`,
    urlTemplate: 'volvox_genes/{refseq}/trackData.json',
    readFile: url => new RemoteFile(url).readFile(),
  })

  for await (const feature of store.getFeatures({
    refName: 'ctgA',
    start: 0,
    end: 50000,
  })) {
    console.log(
      `got feature at ${feature.get('seq_id')}:${feature.get(
        'start',
      )}-${feature.get('end')}`,
    )
  }
})()

API

Table of Contents

• NCListStore
  • Parameters
  • getRegionFeatureDensities
    • Parameters
  • getFeatures
    • Parameters

NCListStore

Sequence feature store using nested containment lists held in JSON files that are lazily read.

Parameters

• args object constructor args

  • args.baseUrl string base URL for resolving relative URLs
  • args.urlTemplate string Template string for the root file of each reference sequence. The reference sequence name will be interpolated into this string where {refseq} appears.
  • args.readFile function function to use for reading remote from URLs.
  • args.cacheSize (optional, default 10)

getRegionFeatureDensities

fetch binned counts of feature coverage in the given region.

Parameters

• query object

  • query.refName string reference sequence name
  • query.start number region start
  • query.end number region end
  • query.numBins number number of bins desired in the feature counts
  • query.basesPerBin number number of bp desired in each feature counting bin

Returns object as: { bins: hist, stats: statEntry }

getFeatures

Fetch features in a given region. This method is an asynchronous generator yielding feature objects.

Parameters

• args object

  • args.refName string reference sequence name
  • args.start number start of region. 0-based half-open.
  • args.end number end of region. 0-based half-open.