@jbrowse/plugin-alignments 1.7.7 → 1.7.8

package/dist/PileupRenderer/PileupRenderer.js

@@ -105,10 +105,14 @@ var alignmentColoring = {
   color_shortinsert: 'pink'
 };
 
-function shouldDrawMismatches(type) {
+function shouldDrawSNPs(type) {
   return !['methylation', 'modifications'].includes(type || '');
 }
 
+function shouldDrawIndels(type) {
+  return true;
+}
+
 var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
   (0, _inherits2.default)(PileupRenderer, _BoxRendererType);
 
@@ -391,7 +395,6 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       });
       var cigar = feature.get('CIGAR');
       var start = feature.get('start');
-      var end = feature.get('end');
       var seq = feature.get('seq');
       var strand = feature.get('strand');
       var cigarOps = (0, _MismatchParser.parseCigar)(cigar);
@@ -412,19 +415,18 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
         try {
           for (_iterator.s(); !(_step = _iterator.n()).done;) {
             var readPos = _step.value;
+            var r = start + readPos;
 
-            if (readPos >= 0 && start + readPos < end) {
-              var _bpSpanPx7 = (0, _util.bpSpanPx)(start + readPos, start + readPos + 1, region, bpPerPx),
-                  _bpSpanPx8 = (0, _slicedToArray2.default)(_bpSpanPx7, 2),
-                  leftPx = _bpSpanPx8[0],
-                  rightPx = _bpSpanPx8[1]; // give it a little boost of 0.1 to not make them fully
-              // invisible to avoid confusion
-
+            var _bpSpanPx7 = (0, _util.bpSpanPx)(r, r + 1, region, bpPerPx),
+                _bpSpanPx8 = (0, _slicedToArray2.default)(_bpSpanPx7, 2),
+                leftPx = _bpSpanPx8[0],
+                rightPx = _bpSpanPx8[1]; // give it a little boost of 0.1 to not make them fully
+            // invisible to avoid confusion
 
-              ctx.fillStyle = base.alpha(probabilities[probIndex] + 0.1).hsl().string();
-              ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx);
-            }
 
+            var prob = probabilities[probIndex];
+            ctx.fillStyle = prob && prob !== 1 ? base.alpha(prob + 0.1).hsl().string() : col;
+            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx);
             probIndex++;
           }
         } catch (err) {
@@ -456,9 +458,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       var seq = feature.get('seq');
       var strand = feature.get('strand');
       var cigarOps = (0, _MismatchParser.parseCigar)(cigar);
-      var rstart = region.start,
-          rend = region.end;
-      var methBins = new Array(rend - rstart).fill(0);
+      var methBins = new Array(region.end - region.start).fill(0);
       var modifications = (0, _MismatchParser.getModificationPositions)(mm, seq, strand);
 
       for (var i = 0; i < modifications.length; i++) {
@@ -473,7 +473,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           try {
             for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
               var pos = _step2.value;
-              var epos = pos + fstart - rstart;
+              var epos = pos + fstart - region.start;
 
               if (epos >= 0 && epos < methBins.length) {
                 methBins[epos] = 1;
@@ -488,7 +488,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       }
 
       for (var j = fstart; j < fend; j++) {
-        var _i = j - rstart;
+        var _i = j - region.start;
 
         if (_i >= 0 && _i < methBins.length) {
           var l1 = regionSequence[_i].toLowerCase();
@@ -498,38 +498,28 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
 
           if (bpPerPx > 2) {
             if (l1 === 'c' && l2 === 'g') {
-              var s = rstart + _i;
+              var s = region.start + _i;
 
               var _bpSpanPx9 = (0, _util.bpSpanPx)(s, s + 2, region, bpPerPx),
                   _bpSpanPx10 = (0, _slicedToArray2.default)(_bpSpanPx9, 2),
                   leftPx = _bpSpanPx10[0],
                   rightPx = _bpSpanPx10[1];
 
-              if (methBins[_i] || methBins[_i + 1]) {
-                ctx.fillStyle = 'red';
-              } else {
-                ctx.fillStyle = 'blue';
-              }
-
+              ctx.fillStyle = methBins[_i] || methBins[_i + 1] ? 'red' : 'blue';
               ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx);
             }
           } // if we are zoomed in, color the c inside the cpg
           else {
             // color
             if (l1 === 'c' && l2 === 'g') {
-              var _s = rstart + _i;
+              var _s = region.start + _i;
 
               var _bpSpanPx11 = (0, _util.bpSpanPx)(_s, _s + 1, region, bpPerPx),
                   _bpSpanPx12 = (0, _slicedToArray2.default)(_bpSpanPx11, 2),
                   _leftPx = _bpSpanPx12[0],
                   _rightPx = _bpSpanPx12[1];
 
-              if (methBins[_i]) {
-                ctx.fillStyle = 'red';
-              } else {
-                ctx.fillStyle = 'blue';
-              }
-
+              ctx.fillStyle = methBins[_i] ? 'red' : 'blue';
               ctx.fillRect(_leftPx, topPx, _rightPx - _leftPx + 0.5, heightPx);
 
               var _bpSpanPx13 = (0, _util.bpSpanPx)(_s + 1, _s + 2, region, bpPerPx),
@@ -537,12 +527,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
                   leftPx2 = _bpSpanPx14[0],
                   rightPx2 = _bpSpanPx14[1];
 
-              if (methBins[_i + 1]) {
-                ctx.fillStyle = 'red';
-              } else {
-                ctx.fillStyle = 'blue';
-              }
-
+              ctx.fillStyle = methBins[_i + 1] ? 'red' : 'blue';
               ctx.fillRect(leftPx2, topPx, rightPx2 - leftPx2 + 0.5, heightPx);
             }
           }
@@ -753,20 +738,9 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       var pxPerBp = Math.min(1 / bpPerPx, 2);
       var w = Math.max(minSubfeatureWidth, pxPerBp);
       var mismatches = feature.get('mismatches');
-      var heightLim = charHeight - 2;
-
-      function getAlphaColor(baseColor, mismatch) {
-        var color = baseColor;
-
-        if (mismatchAlpha && mismatch.qual !== undefined) {
-          color = (0, _color.default)(baseColor).alpha(Math.min(1, mismatch.qual / 50)).hsl().string();
-        }
-
-        return color;
-      } // extraHorizontallyFlippedOffset is used to draw interbase items, which
+      var heightLim = charHeight - 2; // extraHorizontallyFlippedOffset is used to draw interbase items, which
       // are located to the left when forward and right when reversed
 
-
       var extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1; // two pass rendering: first pass, draw all the mismatches except wide
       // insertion markers
 
@@ -785,13 +759,13 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
 
         if (mismatch.type === 'mismatch' && drawSNPs) {
           var baseColor = colorForBase[mismatch.base] || '#888';
-          ctx.fillStyle = getAlphaColor(baseColor, mismatch);
+          ctx.fillStyle = !mismatchAlpha ? baseColor : mismatch.qual !== undefined ? (0, _color.default)(baseColor).alpha(Math.min(1, mismatch.qual / 50)).hsl().string() : baseColor;
           ctx.fillRect(leftPx, topPx, widthPx, heightPx);
 
           if (widthPx >= charWidth && heightPx >= heightLim) {
             // normal SNP coloring
-            var contrast = contrastForBase[mismatch.base] || 'black';
-            ctx.fillStyle = getAlphaColor(contrast, mismatch);
+            var contrastColor = contrastForBase[mismatch.base] || 'black';
+            ctx.fillStyle = !mismatchAlpha ? contrastColor : mismatch.qual !== undefined ? (0, _color.default)(contrastColor).alpha(Math.min(1, mismatch.qual / 50)).hsl().string() : contrastColor;
             ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
           }
         } else if (mismatch.type === 'deletion' && drawIndels) {
@@ -868,12 +842,13 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               ctx.fillStyle = 'purple';
               ctx.fillRect(_leftPx2 - 1, topPx, 2, heightPx);
             } else if (heightPx > charHeight) {
-              var rect = ctx.measureText(_txt);
+              var _rwidth = (0, _util.measureText)(_txt);
+
               var padding = 5;
               ctx.fillStyle = 'purple';
-              ctx.fillRect(_leftPx2 - rect.width / 2 - padding, topPx, rect.width + 2 * padding, heightPx);
+              ctx.fillRect(_leftPx2 - _rwidth / 2 - padding, topPx, _rwidth + 2 * padding, heightPx);
               ctx.fillStyle = 'white';
-              ctx.fillText(_txt, _leftPx2 - rect.width / 2, topPx + heightPx);
+              ctx.fillText(_txt, _leftPx2 - _rwidth / 2, topPx + heightPx);
             } else {
               var _padding = 2;
               ctx.fillStyle = 'purple';
@@ -950,93 +925,82 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
     }
   }, {
     key: "makeImageData",
-    value: function () {
-      var _makeImageData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(ctx, layoutRecords, props) {
-        var _this2 = this;
+    value: function makeImageData(ctx, layoutRecords, props) {
+      var layout = props.layout,
+          config = props.config,
+          showSoftClip = props.showSoftClip,
+          colorBy = props.colorBy,
+          configTheme = props.theme;
+      var mismatchAlpha = (0, _configuration.readConfObject)(config, 'mismatchAlpha');
+      var minSubfeatureWidth = (0, _configuration.readConfObject)(config, 'minSubfeatureWidth');
+      var largeInsertionIndicatorScale = (0, _configuration.readConfObject)(config, 'largeInsertionIndicatorScale');
+      var defaultColor = (0, _configuration.readConfObject)(config, 'color') === '#f0f';
+      var theme = (0, _ui.createJBrowseTheme)(configTheme);
+      var colorForBase = getColorBaseMap(theme);
+      var contrastForBase = getContrastBaseMap(theme);
 
-        var layout, config, showSoftClip, colorBy, configTheme, mismatchAlpha, minSubfeatureWidth, insertScale, defaultColor, theme, colorForBase, contrastForBase, _this$getCharWidthHei2, charWidth, charHeight;
+      if (!layout) {
+        throw new Error("layout required");
+      }
 
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                layout = props.layout, config = props.config, showSoftClip = props.showSoftClip, colorBy = props.colorBy, configTheme = props.theme;
-                mismatchAlpha = (0, _configuration.readConfObject)(config, 'mismatchAlpha');
-                minSubfeatureWidth = (0, _configuration.readConfObject)(config, 'minSubfeatureWidth');
-                insertScale = (0, _configuration.readConfObject)(config, 'largeInsertionIndicatorScale');
-                defaultColor = (0, _configuration.readConfObject)(config, 'color') === '#f0f';
-                theme = (0, _ui.createJBrowseTheme)(configTheme);
-                colorForBase = getColorBaseMap(theme);
-                contrastForBase = getContrastBaseMap(theme);
-
-                if (layout) {
-                  _context.next = 10;
-                  break;
-                }
+      if (!layout.addRect) {
+        throw new Error('invalid layout object');
+      }
 
-                throw new Error("layout required");
+      ctx.font = 'bold 10px Courier New,monospace';
 
-              case 10:
-                if (layout.addRect) {
-                  _context.next = 12;
-                  break;
-                }
+      var _this$getCharWidthHei2 = this.getCharWidthHeight(ctx),
+          charWidth = _this$getCharWidthHei2.charWidth,
+          charHeight = _this$getCharWidthHei2.charHeight;
 
-                throw new Error('invalid layout object');
-
-              case 12:
-                ctx.font = 'bold 10px Courier New,monospace';
-                _this$getCharWidthHei2 = this.getCharWidthHeight(ctx), charWidth = _this$getCharWidthHei2.charWidth, charHeight = _this$getCharWidthHei2.charHeight;
-                layoutRecords.forEach(function (feat) {
-                  if (feat === null) {
-                    return;
-                  }
-
-                  _this2.drawAlignmentRect(ctx, feat, _objectSpread(_objectSpread({}, props), {}, {
-                    defaultColor: defaultColor,
-                    colorForBase: colorForBase,
-                    contrastForBase: contrastForBase,
-                    charWidth: charWidth,
-                    charHeight: charHeight
-                  }));
+      var drawSNPs = shouldDrawSNPs(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
+      var drawIndels = shouldDrawIndels(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
 
-                  _this2.drawMismatches(ctx, feat, props, {
-                    mismatchAlpha: mismatchAlpha,
-                    drawSNPs: shouldDrawMismatches(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type),
-                    drawIndels: shouldDrawMismatches(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type),
-                    largeInsertionIndicatorScale: insertScale,
-                    minSubfeatureWidth: minSubfeatureWidth,
-                    charWidth: charWidth,
-                    charHeight: charHeight,
-                    colorForBase: colorForBase,
-                    contrastForBase: contrastForBase
-                  });
-
-                  if (showSoftClip) {
-                    _this2.drawSoftClipping(ctx, feat, props, config, theme);
-                  }
-                });
+      for (var i = 0; i < layoutRecords.length; i++) {
+        var feat = layoutRecords[i];
 
-              case 15:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
+        if (feat === null) {
+          continue;
+        }
 
-      function makeImageData(_x, _x2, _x3) {
-        return _makeImageData.apply(this, arguments);
+        this.drawAlignmentRect(ctx, feat, _objectSpread(_objectSpread({}, props), {}, {
+          defaultColor: defaultColor,
+          colorForBase: colorForBase,
+          contrastForBase: contrastForBase,
+          charWidth: charWidth,
+          charHeight: charHeight
+        }));
+        this.drawMismatches(ctx, feat, props, {
+          mismatchAlpha: mismatchAlpha,
+          drawSNPs: drawSNPs,
+          drawIndels: drawIndels,
+          largeInsertionIndicatorScale: largeInsertionIndicatorScale,
+          minSubfeatureWidth: minSubfeatureWidth,
+          charWidth: charWidth,
+          charHeight: charHeight,
+          colorForBase: colorForBase,
+          contrastForBase: contrastForBase
+        });
       }
 
-      return makeImageData;
-    }() // we perform a full layout before render as a separate method because the
+      if (showSoftClip) {
+        for (var _i3 = 0; _i3 < layoutRecords.length; _i3++) {
+          var _feat = layoutRecords[_i3];
+
+          if (_feat === null) {
+            continue;
+          }
+
+          this.drawSoftClipping(ctx, _feat, props, config, theme);
+        }
+      }
+    } // we perform a full layout before render as a separate method because the
     // layout determines the height of the canvas that we use to render
 
   }, {
     key: "layoutFeats",
     value: function layoutFeats(props) {
-      var _this3 = this;
+      var _this2 = this;
 
       var layout = props.layout,
           features = props.features,
@@ -1060,8 +1024,8 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       var featureMap = sortedBy !== null && sortedBy !== void 0 && sortedBy.type && region.start === sortedBy.pos ? (0, _sortUtil.sortFeature)(features, sortedBy) : features;
       var heightPx = (0, _configuration.readConfObject)(config, 'height');
       var displayMode = (0, _configuration.readConfObject)(config, 'displayMode');
-      var layoutRecords = (0, _util.iterMap)(featureMap.values(), function (feature) {
-        return _this3.layoutFeature({
+      return (0, _util.iterMap)(featureMap.values(), function (feature) {
+        return _this2.layoutFeature({
           feature: feature,
           layout: layout,
           bpPerPx: bpPerPx,
@@ -1071,47 +1035,46 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           displayMode: displayMode
         });
       }, featureMap.size);
-      return layoutRecords;
     }
   }, {
     key: "fetchSequence",
     value: function () {
-      var _fetchSequence2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(renderProps) {
+      var _fetchSequence2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(renderProps) {
         var sessionId, regions, adapterConfig, sequenceAdapter, _yield$getAdapter, dataAdapter, _regions5, region;
 
-        return _regenerator.default.wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
-            switch (_context2.prev = _context2.next) {
+            switch (_context.prev = _context.next) {
               case 0:
                 sessionId = renderProps.sessionId, regions = renderProps.regions, adapterConfig = renderProps.adapterConfig;
                 sequenceAdapter = adapterConfig.sequenceAdapter;
 
                 if (sequenceAdapter) {
-                  _context2.next = 4;
+                  _context.next = 4;
                   break;
                 }
 
-                return _context2.abrupt("return", undefined);
+                return _context.abrupt("return", undefined);
 
               case 4:
-                _context2.next = 6;
+                _context.next = 6;
                 return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, sequenceAdapter);
 
               case 6:
-                _yield$getAdapter = _context2.sent;
+                _yield$getAdapter = _context.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
                 _regions5 = (0, _slicedToArray2.default)(regions, 1), region = _regions5[0];
-                return _context2.abrupt("return", (0, _util2.fetchSequence)(region, dataAdapter));
+                return _context.abrupt("return", (0, _util2.fetchSequence)(region, dataAdapter));
 
               case 10:
               case "end":
-                return _context2.stop();
+                return _context.stop();
             }
           }
-        }, _callee2, this);
+        }, _callee, this);
       }));
 
-      function fetchSequence(_x4) {
+      function fetchSequence(_x) {
         return _fetchSequence2.apply(this, arguments);
       }
 
@@ -1120,21 +1083,21 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
   }, {
     key: "render",
     value: function () {
-      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(renderProps) {
+      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(renderProps) {
         var _renderProps$colorBy,
-            _this4 = this;
+            _this3 = this;
 
         var features, layout, regions, bpPerPx, layoutRecords, _regions6, region, regionSequence, end, start, width, height, res, results;
 
-        return _regenerator.default.wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
-            switch (_context3.prev = _context3.next) {
+            switch (_context2.prev = _context2.next) {
               case 0:
-                _context3.next = 2;
+                _context2.next = 2;
                 return this.getFeatures(renderProps);
 
               case 2:
-                features = _context3.sent;
+                features = _context2.sent;
                 layout = this.createLayoutInWorker(renderProps);
                 regions = renderProps.regions, bpPerPx = renderProps.bpPerPx;
                 layoutRecords = this.layoutFeats(_objectSpread(_objectSpread({}, renderProps), {}, {
@@ -1145,29 +1108,29 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
                 // cases
 
                 if (!(features.size && (0, _util2.shouldFetchReferenceSequence)((_renderProps$colorBy = renderProps.colorBy) === null || _renderProps$colorBy === void 0 ? void 0 : _renderProps$colorBy.type))) {
-                  _context3.next = 13;
+                  _context2.next = 13;
                   break;
                 }
 
-                _context3.next = 10;
+                _context2.next = 10;
                 return this.fetchSequence(renderProps);
 
               case 10:
-                _context3.t0 = _context3.sent;
-                _context3.next = 14;
+                _context2.t0 = _context2.sent;
+                _context2.next = 14;
                 break;
 
               case 13:
-                _context3.t0 = undefined;
+                _context2.t0 = undefined;
 
               case 14:
-                regionSequence = _context3.t0;
+                regionSequence = _context2.t0;
                 end = region.end, start = region.start;
                 width = (end - start) / bpPerPx;
                 height = Math.max(layout.getTotalHeight(), 1);
-                _context3.next = 20;
+                _context2.next = 20;
                 return (0, _offscreenCanvasUtils.renderToAbstractCanvas)(width, height, renderProps, function (ctx) {
-                  return _this4.makeImageData(ctx, layoutRecords, _objectSpread(_objectSpread({}, renderProps), {}, {
+                  return _this3.makeImageData(ctx, layoutRecords, _objectSpread(_objectSpread({}, renderProps), {}, {
                     layout: layout,
                     features: features,
                     regionSequence: regionSequence
@@ -1175,8 +1138,8 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
                 });
 
               case 20:
-                res = _context3.sent;
-                _context3.next = 23;
+                res = _context2.sent;
+                _context2.next = 23;
                 return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupRenderer.prototype), "render", this).call(this, _objectSpread(_objectSpread(_objectSpread({}, renderProps), res), {}, {
                   features: features,
                   layout: layout,
@@ -1185,8 +1148,8 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
                 }));
 
               case 23:
-                results = _context3.sent;
-                return _context3.abrupt("return", _objectSpread(_objectSpread(_objectSpread({}, results), res), {}, {
+                results = _context2.sent;
+                return _context2.abrupt("return", _objectSpread(_objectSpread(_objectSpread({}, results), res), {}, {
                   features: new Map(),
                   layout: layout,
                   height: height,
@@ -1196,13 +1159,13 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
 
               case 25:
               case "end":
-                return _context3.stop();
+                return _context2.stop();
             }
           }
-        }, _callee3, this);
+        }, _callee2, this);
       }));
 
-      function render(_x5) {
+      function render(_x2) {
         return _render.apply(this, arguments);
       }
 

package/dist/PileupRenderer/configSchema.js

@@ -31,8 +31,8 @@ var _default = (0, _configuration.ConfigurationSchema)('PileupRenderer', {
   },
   minSubfeatureWidth: {
     type: 'number',
-    description: 'the minimum width in px for a pileup mismatch feature. use for increasing mismatch marker widths when zoomed out to e.g. 1px or 0.5px',
-    defaultValue: 0
+    description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
+    defaultValue: 0.7
   },
   maxHeight: {
     type: 'integer',

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -20,6 +20,10 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }): Promise<{
         bins: {
             total: number;
+            ref: number;
+            '-1': 0;
+            '0': 0;
+            '1': 0;
             lowqual: {
                 total: number;
                 strands: {
@@ -44,12 +48,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                     [key: string]: number;
                 };
             };
-            ref: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
         }[];
         skipmap: {
             [key: string]: {