Fix for CRAM regularizing failing

src/JBrowse/Browser.js

@@ -730,6 +730,13 @@ regularizeReferenceName: function( refname ) {
         return refname;
 
     refname = refname.toLowerCase()
+
+    // special case of double regularizing behaving badly
+    if(refname.match(/^chrm/)) {
+        return 'chrm'
+    }
+
+    refname = refname
                      .replace(/^chro?m?(osome)?/,'chr')
                      .replace(/^co?n?ti?g/,'ctg')
                      .replace(/^scaff?o?l?d?/,'scaffold')

src/JBrowse/Store/SeqFeature/CRAM.js

@@ -21,7 +21,6 @@ class CramSlightlyLazyFeature {
     _get_strand() { return this.record.isReverseComplemented() ? -1 : 1 }
     _get_read_group_id() { return this.record.readGroupId }
     _get_qual() { return (this.record.qualityScores || []).map(q => q+33).join(' ')}
-    _get_seq() { return this.record.readBases}
     _get_seq_id() { return this._store._refIdToName(this.record.sequenceId)}
     _get_qc_failed() { return this.record.isFailedQc()}
     _get_secondary_alignment() { return this.record.isSecondary()}

src/JBrowse/Store/SeqFeature/IndexedFasta.js

@@ -70,7 +70,12 @@ return declare( [ SeqFeatureStore, DeferredFeaturesMixin ],
         if(query.start < 0) {
             query.start = 0;
         }
-        this.fasta.getResiduesByName( this.refSeq.name, query.start, query.end ).then((seq) => {
+        var refname = query.ref;
+        // if they both regularize to the same thing, use this.refSeq.name since that is guaranteed to be from refseq store
+        if(!this.browser.compareReferenceNames( this.refSeq.name, refname ) )
+            refname = this.refSeq.name;
+
+        this.fasta.getResiduesByName( refname, query.start, query.end ).then(seq => {
             featCallback(new SimpleFeature({data: {seq, start: query.start, end: query.end}}))
             endCallback()
         },

src/JBrowse/Store/SeqFeature/SequenceChunks.js

@@ -48,6 +48,7 @@ return declare( SeqFeatureStore,
         errorCallback = errorCallback || function(e) { console.error(e); };
 
         var refname = query.ref;
+        // if they both regularize to the same thing, use this.refSeq.name since that is guaranteed to be from refseq store
         if( ! this.browser.compareReferenceNames( this.refSeq.name, refname ) )
             refname = this.refSeq.name;
 

src/JBrowse/Store/SeqFeature/TwoBit.js

@@ -79,7 +79,12 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin], {
         if (start < 0) {
             start = 0
         }
-        this.twoBit.getSequence(query.ref, start, query.end)
+        var refname = query.ref;
+        // if they both regularize to the same thing, use this.refSeq.name since that is guaranteed to be from refseq store
+        if(!this.browser.compareReferenceNames( this.refSeq.name, refname ) )
+            refname = this.refSeq.name;
+
+        this.twoBit.getSequence(refname, start, query.end)
             .then(seq => {
                 if (seq !== undefined) {
                     featCallback(new SimpleFeature({

tests/js_tests/spec/RegularizeRefSeqs.spec.js

@@ -9,7 +9,14 @@ describe( 'centralized ref seq name regularization', function() {
 
     var testCases = [
         [ 'ctgA', 'ctga' ],
+        [ 'MT', 'chrm' ],
+        [ 'Pt', 'pt' ],
+        [ 'C9', 'c9' ],
+        [ 'chrM', 'chrm' ],
+        [ 'chrMT', 'chrm' ],
+        [ 'ChrC', 'chrc' ],
         [ 'chrom01', 'chr1' ],
+        [ 'Bvchr1_un.sca002', 'bvchr1_un.sca002' ],
         [ 'chr01', 'chr1' ],
         [ 'CHROMOSOME11', 'chr11' ],
         [ 'SCAFFOLD0231', 'scaffold231' ],
@@ -19,11 +26,21 @@ describe( 'centralized ref seq name regularization', function() {
         [ '01', 'chr1' ],
         [ '1', 'chr1' ]
     ];
+
+
+
     array.forEach( testCases, function( testCase ) {
         it( 'works for '+testCase[0], function() {
             expect( b.regularizeReferenceName( testCase[0] ) ).toEqual( testCase[1] );
         });
     });
 
+    array.forEach( testCases, function( testCase ) {
+        it( 'double regularizing works for '+testCase[1], function() {
+            expect( b.regularizeReferenceName( testCase[1] ) ).toEqual( testCase[1] );
+        });
+    });
+})
+
 });
-});
+

tests/js_tests/spec/TwoBit.spec.js

@@ -10,11 +10,12 @@ require([
             aspect,
             XHRBlob
         ) {
-    
+
 describe(".2bit data store with T_ko.2bit", function() {
 
     var t = new TwoBitStore({
             browser: new Browser({ unitTestMode: true }),
+            refSeq: { name: 'chr1', start: 1, end: 500001 },
             blob: new XHRBlob("../data/T_ko.2bit")
         });
 
@@ -55,17 +56,18 @@ describe(".2bit data store with T_ko.2bit", function() {
             function() { done = true; });
 
         waitsFor( function() { return done; }, 2000);
-        runs(function(){ 
+        runs(function(){
             expect(features.length).toEqual(0);
         });
     });
-   
+
 });
 
 describe(".2bit data store with volvox.2bit", function() {
 
     var t2 = new TwoBitStore({
             browser: new Browser({ unitTestMode: true }),
+            refSeq: { name: 'chr1', start: 1, end: 500001 },
             blob: new XHRBlob("../data/volvox.2bit")
         });
 
@@ -122,19 +124,20 @@ describe(".2bit data store with volvox.2bit", function() {
             function() { done = true; });
 
         waitsFor( function() { return done; }, 2000);
-        runs(function(){ 
+        runs(function(){
             expect(features.length).toEqual(0);
         });
     });
-   
+
 });
 
     var seqString = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCTATCTATCTATCTATCTATCTTTTTCCCCCCGGGGGGagagagagactctagcatcctcctacctcacNNacCNctTGGACNCcCaGGGatttcNNNcccNNCCNCgN";
 
 describe(".2bit data store with random data foo.2bit", function() {
-    
+
     var t3 = new TwoBitStore({
         browser: new Browser({unitTestMode: true }),
+        refSeq: { name: 'chr1', start: 1, end: 500001 },
         blob: new XHRBlob("../data/foo.2bit")
     });
 
@@ -182,6 +185,7 @@ describe(".2bit data store with random data foo.2bit", function() {
 describe("empty 2bit", function() {
     var t4 = new TwoBitStore({
         browser: new Browser({ unitTestMode: true }),
+        refSeq: { name: 'chr1', start: 1, end: 500001 },
         blob: new XHRBlob("../data/empty.2bit")
     });
 
@@ -192,9 +196,9 @@ describe("empty 2bit", function() {
     it("returns no data, but doesn't crash", function() {
         var done;
         var features = [];
-        t4.getFeatures({ref: "unimportant", start: 0, end: 4000}, 
+        t4.getFeatures({ref: "unimportant", start: 0, end: 4000},
             function(feature) {
-                features.push(feature); 
+                features.push(feature);
             },
             function() { done = true; },
             function(err) { console.log(err); });