@jbrowse/plugin-alignments 1.6.1 → 1.6.5

package/dist/plugin-alignments.esm.js

@@ -2073,7 +2073,7 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "generateCoverageBins",
     value: function () {
       var _generateCoverageBins = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5(features, region, opts) {
-        var colorBy, _yield$this$configure3, sequenceAdapter, originalRefName, refName, start, end, binMax, skipmap, initBins, regionSeq, _yield$sequenceAdapte, _yield$sequenceAdapte2, feat, bins;
+        var colorBy, _yield$this$configure3, sequenceAdapter, originalRefName, refName, start, end, binMax, skipmap, regionSeq, _yield$sequenceAdapte, _yield$sequenceAdapte2, feat, bins;
 
         return runtime_1.wrap(function _callee5$(_context5) {
           while (1) {
@@ -2088,41 +2088,29 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 sequenceAdapter = _yield$this$configure3.sequenceAdapter;
                 originalRefName = region.originalRefName, refName = region.refName, start = region.start, end = region.end;
                 binMax = Math.ceil(region.end - region.start);
-                skipmap = {};
-                initBins = Array.from({
-                  length: binMax
-                }, function () {
-                  return {
-                    total: 0,
-                    lowqual: {},
-                    cov: {},
-                    delskips: {},
-                    noncov: {},
-                    ref: {}
-                  };
-                }); // request an extra +1 on the end to get CpG crossing region boundary
+                skipmap = {}; // request an extra +1 on the end to get CpG crossing region boundary
 
                 if (!sequenceAdapter) {
-                  _context5.next = 16;
+                  _context5.next = 15;
                   break;
                 }
 
-                _context5.next = 12;
+                _context5.next = 11;
                 return sequenceAdapter.getFeatures({
                   refName: originalRefName || refName,
                   start: start,
                   end: end + 1,
-                  assemblyName: 'na'
+                  assemblyName: region.assemblyName
                 }).pipe(toArray()).toPromise();
 
-              case 12:
+              case 11:
                 _yield$sequenceAdapte = _context5.sent;
                 _yield$sequenceAdapte2 = _slicedToArray(_yield$sequenceAdapte, 1);
                 feat = _yield$sequenceAdapte2[0];
                 regionSeq = feat === null || feat === void 0 ? void 0 : feat.get('seq');
 
-              case 16:
-                _context5.next = 18;
+              case 15:
+                _context5.next = 17;
                 return features.pipe(reduce(function (bins, feature) {
                   var cigar = feature.get('CIGAR');
                   var fstart = feature.get('start');
@@ -2133,10 +2121,18 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   for (var j = fstart; j < fend; j++) {
                     var i = j - region.start;
 
-                    if (i >= 0 && i < bins.length) {
-                      var bin = bins[i];
+                    if (i >= 0 && i < binMax) {
+                      var bin = bins[i] || {
+                        total: 0,
+                        lowqual: {},
+                        cov: {},
+                        delskips: {},
+                        noncov: {},
+                        ref: {}
+                      };
                       bin.total++;
                       inc(bin, fstrand, 'ref', 'ref');
+                      bins[i] = bin;
                     }
                   }
 
@@ -2299,7 +2295,7 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                             start: start,
                             end: end,
                             strand: strand,
-                            xs: feature.get('xs') || feature.get('ts') || feature.get('tags').XS || feature.get('tags').TS,
+                            xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
                             score: 1
                           };
                         } else {
@@ -2310,16 +2306,16 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   }
 
                   return bins;
-                }, initBins)).toPromise();
+                }, [])).toPromise();
 
-              case 18:
+              case 17:
                 bins = _context5.sent;
                 return _context5.abrupt("return", {
                   bins: bins,
                   skipmap: skipmap
                 });
 
-              case 20:
+              case 19:
               case "end":
                 return _context5.stop();
             }
@@ -3459,16 +3455,16 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
             ctx.fillText("(".concat(mismatch.base, ")"), leftPx + 2, topPx + heightPx);
           }
         } else if (mismatch.type === 'skip') {
-          // fix to avoid bad rendering
-          // note that this was also related to chrome bug https://bugs.chromium.org/p/chro>
-          // ref #1236
+          // fix to avoid bad rendering note that this was also related to chrome
+          // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528
+          // also affected firefox ref #1236 #2750
           if (leftPx + widthPx > 0) {
             // make small exons more visible when zoomed far out
-            ctx.clearRect(leftPx, topPx, widthPx - (bpPerPx > 10 ? 1.5 : 0), heightPx);
+            var adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
+            ctx.clearRect(leftPx, topPx, adjustPx, heightPx);
+            ctx.fillStyle = '#333';
+            ctx.fillRect(Math.max(0, leftPx), topPx + heightPx / 2 - 1, adjustPx + (leftPx < 0 ? leftPx : 0), 2);
           }
-
-          ctx.fillStyle = '#333';
-          ctx.fillRect(leftPx, topPx + heightPx / 2, widthPx, 2);
         }
       } // second pass, draw wide insertion markers on top
 
@@ -7417,7 +7413,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "estimateRegionsStats",
     value: function () {
       var _estimateRegionsStats = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee9(regions, opts) {
-        var _yield$this$configure4, bam, index, bytes, fetchSizeLimit;
+        var _yield$this$configure4, bam, bytes, fetchSizeLimit;
 
         return runtime_1.wrap(function _callee9$(_context9) {
           while (1) {
@@ -7429,18 +7425,16 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
               case 2:
                 _yield$this$configure4 = _context9.sent;
                 bam = _yield$this$configure4.bam;
-                // @ts-ignore
-                index = bam.index; // this is a method to avoid calling on htsget adapters
 
-                if (!(index.filehandle !== '?')) {
-                  _context9.next = 13;
+                if (!(bam.index.filehandle !== '?')) {
+                  _context9.next = 12;
                   break;
                 }
 
-                _context9.next = 8;
-                return bytesForRegions(regions, index);
+                _context9.next = 7;
+                return bytesForRegions(regions, bam);
 
-              case 8:
+              case 7:
                 bytes = _context9.sent;
                 fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit');
                 return _context9.abrupt("return", {
@@ -7448,10 +7442,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   fetchSizeLimit: fetchSizeLimit
                 });
 
-              case 13:
+              case 12:
                 return _context9.abrupt("return", _get(_getPrototypeOf(BamAdapter.prototype), "estimateRegionsStats", this).call(this, regions, opts));
 
-              case 14:
+              case 13:
               case "end":
                 return _context9.stop();
             }