nclist-js
Read legacy JBrowse 1 nested containment list JSON.
Status
Usage
import { RemoteFile } from 'generic-filehandle'
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
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, default10
)
-
getRegionFeatureDensities
fetch binned counts of feature coverage in the given region.
Parameters
-
query
object
Returns object as:
{ bins: hist, stats: statEntry }
getFeatures
Fetch features in a given region. This method is an asynchronous generator yielding feature objects.