Add Bgzf fasta

src/JBrowse/Store/SeqFeature/BgzipIndexedFasta.js

@@ -0,0 +1,86 @@
+const LRU = cjsRequire('lru-cache')
+const { BgzipIndexedFasta } = cjsRequire('@gmod/fasta')
+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.fasta)
+            dataBlob = new BlobFilehandleWrapper(args.fasta)
+        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}`
+        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
+        };
+    }
+
+});
+});

src/JBrowse/Store/SeqFeature/IndexedFasta.js

@@ -40,7 +40,7 @@ return declare( [ SeqFeatureStore, DeferredFeaturesMixin ],
      * served as static text files.
      * @constructs
      */
-    constructor: async function(args) {
+    constructor: function(args) {
         let dataBlob
         if (args.fasta)
             dataBlob = new BlobFilehandleWrapper(args.fasta)
@@ -70,7 +70,7 @@ return declare( [ SeqFeatureStore, DeferredFeaturesMixin ],
                 fai: indexBlob
             })
 
-            fastaIndexedFilesCache.set(cacheKey, this.cram)
+            fastaIndexedFilesCache.set(cacheKey, this.fasta)
         }
         this.fasta.getSequenceList().then(
             () => this._deferred.features.resolve({success:true}),
@@ -88,13 +88,13 @@ return declare( [ SeqFeatureStore, DeferredFeaturesMixin ],
 
     getRefSeqs: function( featCallback, errorCallback ) {
         this.fasta.getSequenceSizes().then((seqs) => {
-            console.log(seqs);
             featCallback(seqs);
         }, errorCallback);
     },
     saveStore: function() {
         return {
-            urlTemplate: (this.config.file||this.config.blob).url
+            urlTemplate: (this.config.file||this.config.blob).url,
+            faiUrlTemplate: this.config.fai.url
         };
     }