update gff3 and vcf tabix stores to use @gmod/tabix

src/JBrowse/Model/BGZip/BGZBlob.js

@@ -135,4 +135,4 @@ var BGZBlob = declare( null,
 });
 
 return BGZBlob;
-});
+});

src/JBrowse/Store/SeqFeature/GFF3Tabix.js

@@ -71,9 +71,9 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
             })
 
         // start our global stats estimation
-        this.getHeader()
+        this.indexedData.featureCount('nonexistent')
             .then(
-                header => {
+                () => {
                     this._deferred.features.resolve({ success: true })
                     this._estimateGlobalStats()
                         .then(
@@ -88,33 +88,8 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
             )
     },
 
-    getHeader() {
-        if (this._parsedHeader) return this._parsedHeader
-
-        this._parsedHeader = new Deferred()
-        const reject = this._parsedHeader.reject.bind(this._parsedHeader)
-
-        this.indexedData.indexLoaded
-            .then( () => {
-                const maxFetch = this.indexedData.index.firstDataLine
-                    ? this.indexedData.index.firstDataLine.block + this.indexedData.data.blockSize - 1
-                    : null
-
-                this.indexedData.data.read(
-                    0,
-                    maxFetch,
-                    bytes => this._parsedHeader.resolve( this.header ),
-                    reject
-                );
-            },
-            reject
-        )
-
-        return this._parsedHeader
-    },
-
     _getFeatures(query, featureCallback, finishedCallback, errorCallback, allowRedispatch = true) {
-        this.getHeader().then(
+        this.indexedData.featureCount('nonexistent').then(
             () => {
                 const lines = []
                 this.indexedData.getLines(

src/JBrowse/Store/SeqFeature/IndexedStatsEstimationMixin.js

@@ -20,24 +20,21 @@ return declare( GlobalStats, {
      * estimate the feature density of the store.
      * @private
      */
-    _estimateGlobalStats: function( refseq ) {
-        refseq = refseq || this.refSeq;
-        var featCount;
-        if(this.indexedData) {
-            featCount = this.indexedData.featureCount(refseq.name);
-        } else if(this.bam) {
-            var chr = refseq.name;
-            chr = this.browser.regularizeReferenceName( chr );
-            var chrId = this.bam.chrToIndex && this.bam.chrToIndex[chr];
-            featCount = this.bam.index.featureCount(chrId, true);
+    async _estimateGlobalStats(refseq) {
+        refseq = refseq || this.refSeq
+        let featCount
+        if (this.indexedData) {
+            featCount = await this.indexedData.featureCount(refseq.name)
+        } else if (this.bam) {
+            const chr = this.browser.regularizeReferenceName(refseq.name)
+            const chrId = this.bam.chrToIndex && this.bam.chrToIndex[chr]
+            featCount = await this.bam.index.featureCount(chrId, true)
         }
-        if(featCount == -1) {
-            return this.inherited(arguments);
+        if (featCount == -1) {
+            return this.inherited('_estimateGlobalStats', arguments)
         }
-        var density = featCount / (refseq.end - refseq.start);
-        var deferred = new Deferred();
-        deferred.resolve({ featureDensity: density });
-        return deferred;
+        const featureDensity = featCount / (refseq.end - refseq.start)
+        return { featureDensity }
     }
 
 });

src/JBrowse/Store/SeqFeature/VCFTabix.js

@@ -1,3 +1,7 @@
+const promisify = cjsRequire('util.promisify')
+const zlib = cjsRequire('zlib')
+const gunzip = promisify(zlib.gunzip)
+
 define([
            'dojo/_base/declare',
            'dojo/_base/lang',
@@ -29,7 +33,7 @@ define([
 // files don't actually have an end coordinate, so we have to make it
 // here.  also convert coordinates to interbase.
 var VCFIndexedFile = declare( TabixIndexedFile, {
-    parseLine: function() {
+    parseLine() {
         var i = this.inherited( arguments );
         if( i ) {
             var ret = i.fields[7].match(/^END=(\d+)|;END=(\d+)/);
@@ -43,7 +47,7 @@ var VCFIndexedFile = declare( TabixIndexedFile, {
 return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, IndexedStatsEstimationMixin, VCFParser ],
 {
 
-    constructor: function( args ) {
+    constructor( args ) {
         var thisB = this;
         var csiBlob, tbiBlob;
 
@@ -69,6 +73,8 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                 { expectRanges: true }
             );
 
+        this.fileBlob = fileBlob
+
         this.indexedData = new VCFIndexedFile(
             {
                 tbi: tbiBlob,
@@ -97,35 +103,15 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
     },
 
     /** fetch and parse the VCF header lines */
-    getVCFHeader: function() {
-        var thisB = this;
-        return this._parsedHeader || ( this._parsedHeader = function() {
-            var d = new Deferred();
-            var reject = lang.hitch( d, 'reject' );
-
-            thisB.indexedData.indexLoaded.then( function() {
-                var maxFetch = thisB.indexedData.index.firstDataLine
-                    ? thisB.indexedData.index.firstDataLine.block + thisB.indexedData.data.blockSize - 1
-                    : null;
-
-                thisB.indexedData.data.read(
-                    0,
-                    maxFetch,
-                    function( bytes ) {
-                        thisB.parseHeader( new Uint8Array( bytes ) );
-                        d.resolve( thisB.header );
-                    },
-                    reject
-                );
-             },
-             reject
-            );
-
-            return d;
-        }.call(this));
+    getVCFHeader() {
+        if (!this._parsedHeader) {
+            this._parsedHeader = this.indexedData.getHeader()
+                .then(headerBytes => this.parseHeader(headerBytes))
+        }
+        return this._parsedHeader
     },
 
-    _getFeatures: function( query, featureCallback, finishedCallback, errorCallback ) {
+    _getFeatures( query, featureCallback, finishedCallback, errorCallback ) {
         var thisB = this;
         thisB.getVCFHeader().then( function() {
             thisB.indexedData.getLines(
@@ -152,12 +138,12 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
      * smart enough to regularize reference sequence names, while
      * others are not.
      */
-    hasRefSeq: function( seqName, callback, errorCallback ) {
+    hasRefSeq( seqName, callback, errorCallback ) {
         return this.indexedData.index.hasRefSeq( seqName, callback, errorCallback );
     },
 
 
-    saveStore: function() {
+    saveStore() {
         return {
             urlTemplate: this.config.file.url,
             tbiUrlTemplate: ((this.config.tbi)||{}).url,