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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| const LRU = cjsRequire('lru-cache') | ||
| const { BgzipIndexedFasta } = cjsRequire('@gmod/indexedfasta') | ||
| const { Buffer } = cjsRequire('buffer') | ||
|
|
||
| const fastaIndexedFilesCache = LRU(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 | ||
| }) | ||
|
|
||
| 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 | ||
| }; | ||
| } | ||
|
|
||
| }); | ||
| }); |
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