@gmod/nclist/README.md

Read features from JBrowse 1 format nested containment list JSON

# nclist-js

Read legacy JBrowse 1 nested containment list JSON.

## Status

[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/nclist-js/push.yml?branch=master)](https://github.com/GMOD/nclist-js/actions)
[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/nclist-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/nclist-js/branch/master)
[![NPM version](https://img.shields.io/npm/v/@gmod/nclist.svg?logo=npm\&style=flat-square)](https://npmjs.org/package/@gmod/nclist)

## Usage

```javascript
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

<!-- Generated by documentation.js. Update this documentation by updating the source code. -->

#### Table of Contents

*   [NCListStore](#ncliststore)
    *   [Parameters](#parameters)
    *   [getRegionFeatureDensities](#getregionfeaturedensities)
        *   [Parameters](#parameters-1)
    *   [getFeatures](#getfeatures)
        *   [Parameters](#parameters-2)

### NCListStore

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

#### Parameters

*   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** constructor args

    *   `args.baseUrl` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** base URL for resolving relative URLs
    *   `args.urlTemplate` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/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](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/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](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;

    *   `query.refName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** reference sequence name
    *   `query.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** region start
    *   `query.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** region end
    *   `query.numBins` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** number of bins desired in the feature counts
    *   `query.basesPerBin` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** number of bp desired in each feature counting bin

Returns **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/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](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;

    *   `args.refName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** reference sequence name
    *   `args.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of region. 0-based half-open.
    *   `args.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of region. 0-based half-open.