nclist-js

Read legacy JBrowse 1 nested containment list JSON.

Status


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

#### Table of Contents

* NCListStore
* Parameters
* getRegionFeatureDensities
* Parameters
* getFeatures
* Parameters

$3

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.