@gmod/jbrowse/src/JBrowse/Store/SeqFeature/BgzipIndexedFasta.js

JBrowse - client-side genome browser

const LRU = cjsRequire('quick-lru')
const { BgzipIndexedFasta } = cjsRequire('@gmod/indexedfasta')
const { Buffer } = cjsRequire('buffer')

const fastaIndexedFilesCache = new LRU({ maxSize: 5 })

const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper')

define( [ 'dojo/_base/declare',
          'dojo/_base/lang',
          'JBrowse/Model/XHRBlob',
          'JBrowse/Store/SeqFeature/IndexedFasta'
        ],
        function(
            declare,
            lang,
            XHRBlob,
            IndexedFasta
        ) {

return declare( IndexedFasta,
{

    /**
     * Storage backend for sequences in indexed fasta files
     * served as static text files.
     * @constructs
     */
    constructor: function(args) {
        let dataBlob
        if (args.bgzfa)
            dataBlob = new BlobFilehandleWrapper(args.bgzfa)
        else if (args.urlTemplate)
            dataBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate), { expectRanges: true }))
        else
            dataBlob = new BlobFilehandleWrapper(new XHRBlob('data.fa', { expectRanges: true }))

        let indexBlob
        if (args.fai)
            indexBlob = new BlobFilehandleWrapper(args.fai)
        else if (args.faiUrlTemplate)
            indexBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.faiUrlTemplate)))
        else if (args.urlTemplate)
            indexBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate+'.fai')))
        else throw new Error('no index provided, must provide a FASTA index')


        let gziBlob
        if(args.gzi)
            gziBlob = new BlobFilehandleWrapper(args.gzi)
        else if(args.gziUrlTemplate)
            gziBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.gziUrlTemplate)))
        else if (args.urlTemplate)
            gziBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate+'.gzi')))
        else throw new Error('no gzi index provided, must provide a GZI index')

        this.source = dataBlob.toString()

        // LRU-cache the CRAM object so we don't have to re-download the
        // index when we switch chromosomes
        const cacheKey = `data: ${dataBlob}, index: ${indexBlob}, gzi: ${gziBlob}`
        this.fasta = fastaIndexedFilesCache.get(cacheKey)
        if (!this.fasta) {
            this.fasta = new BgzipIndexedFasta({
                fasta: dataBlob,
                fai: indexBlob,
                gzi: gziBlob,
                chunkSizeLimit: args.chunkSizeLimit || 1000000
            })

            fastaIndexedFilesCache.set(cacheKey, this.fasta)
        }
        this.fasta.getSequenceList().then(
            () => this._deferred.features.resolve({success:true}),
            () => this._failAllDeferred()
        )
    },
    saveStore: function() {
        return {
            urlTemplate: (this.config.file||this.config.blob).url,
            faiUrlTemplate: this.config.fai.url,
            gziUrlTemplate: this.config.gzi.url
        };
    }

});
});