@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,296 +1,271 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _ui = require("@jbrowse/core/ui");
-
-var _util = require("@jbrowse/core/util");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _pluginWiggle = require("@jbrowse/plugin-wiggle");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
-var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
-  (0, _inherits2.default)(SNPCoverageRenderer, _WiggleBaseRenderer);
-
-  var _super = _createSuper(SNPCoverageRenderer);
-
-  function SNPCoverageRenderer() {
-    (0, _classCallCheck2.default)(this, SNPCoverageRenderer);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(SNPCoverageRenderer, [{
-    key: "draw",
-    value: // note: the snps are drawn on linear scale even if the data is drawn in log
-    // scape hence the two different scales being used
-    function draw(ctx, props) {
-      var features = props.features,
-          regions = props.regions,
-          bpPerPx = props.bpPerPx,
-          displayCrossHatches = props.displayCrossHatches,
-          _props$modificationTa = props.modificationTagMap,
-          modificationTagMap = _props$modificationTa === void 0 ? {} : _props$modificationTa,
-          scaleOpts = props.scaleOpts,
-          unadjustedHeight = props.height,
-          configTheme = props.theme,
-          cfg = props.config,
-          ticks = props.ticks;
-      var theme = (0, _ui.createJBrowseTheme)(configTheme);
-
-      var _regions = (0, _slicedToArray2.default)(regions, 1),
-          region = _regions[0];
-
-      var width = (region.end - region.start) / bpPerPx; // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-      // wiggle display, and makes the height of the actual drawn area add
-      // "padding" to the top and bottom of the display
-
-      var offset = _pluginWiggle.YSCALEBAR_LABEL_OFFSET;
-      var height = unadjustedHeight - offset * 2;
-      var domain = scaleOpts.domain;
-
-      if (!domain) {
-        return;
-      }
-
-      var opts = _objectSpread(_objectSpread({}, scaleOpts), {}, {
-        range: [0, height]
-      });
-
-      var viewScale = (0, _pluginWiggle.getScale)(opts); // clipping and insertion indicators, uses a smaller height/2 scale
-
-      var indicatorViewScale = (0, _pluginWiggle.getScale)(_objectSpread(_objectSpread({}, opts), {}, {
-        range: [0, height / 2],
-        scaleType: 'linear'
-      }));
-      var originY = (0, _pluginWiggle.getOrigin)(scaleOpts.scaleType);
-      var indicatorThreshold = (0, _configuration.readConfObject)(cfg, 'indicatorThreshold');
-      var drawInterbaseCounts = (0, _configuration.readConfObject)(cfg, 'drawInterbaseCounts');
-      var drawArcs = (0, _configuration.readConfObject)(cfg, 'drawArcs');
-      var drawIndicators = (0, _configuration.readConfObject)(cfg, 'drawIndicators'); // get the y coordinate that we are plotting at, this can be log scale
-
-      var toY = function toY(n) {
-        return height - (viewScale(n) || 0) + offset;
-      };
-
-      var toHeight = function toHeight(n) {
-        return toY(originY) - toY(n);
-      };
-
-      var indicatorToY = function indicatorToY(n) {
-        return height - (indicatorViewScale(n) || 0) + offset;
-      };
-
-      var indicatorToHeight = function indicatorToHeight(n) {
-        return indicatorToY((0, _pluginWiggle.getOrigin)('linear')) - indicatorToY(n);
-      };
-
-      var colorForBase = {
-        A: theme.palette.bases.A.main,
-        C: theme.palette.bases.C.main,
-        G: theme.palette.bases.G.main,
-        T: theme.palette.bases.T.main,
-        total: 'lightgrey',
-        insertion: 'purple',
-        softclip: 'blue',
-        hardclip: 'red',
-        meth: 'red',
-        unmeth: 'blue',
-        ref: 'lightgrey'
-      };
-      var feats = (0, _toConsumableArray2.default)(features.values());
-      var coverage = feats.filter(function (f) {
-        return f.get('type') !== 'skip';
-      });
-      var skips = feats.filter(function (f) {
-        return f.get('type') === 'skip';
-      }); // Use two pass rendering, which helps in visualizing the SNPs at higher
-      // bpPerPx First pass: draw the gray background
-
-      ctx.fillStyle = colorForBase.total;
-
-      for (var i = 0; i < coverage.length; i++) {
-        var feature = coverage[i];
-
-        var _featureSpanPx = (0, _util.featureSpanPx)(feature, region, bpPerPx),
-            _featureSpanPx2 = (0, _slicedToArray2.default)(_featureSpanPx, 2),
-            leftPx = _featureSpanPx2[0],
-            rightPx = _featureSpanPx2[1];
-
-        var w = rightPx - leftPx + 0.3;
-        var score = feature.get('score');
-        ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-      } // Keep track of previous total which we will use it to draw the interbase
-      // indicator (if there is a sudden clip, there will be no read coverage but
-      // there will be "clip" coverage) at that position beyond the read. if the
-      // clip is right at a block boundary then prevTotal will not be available,
-      // so this is a best attempt to plot interbase indicator at the "cliffs"
-
-
-      var prevTotal = 0; // 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 : 0; // Second pass: draw the SNP data, and add a minimum feature width of 1px
-      // which can be wider than the actual bpPerPx This reduces overdrawing of
-      // the grey background over the SNPs
-
-      for (var _i = 0; _i < coverage.length; _i++) {
-        var _feature = coverage[_i];
-
-        var _featureSpanPx3 = (0, _util.featureSpanPx)(_feature, region, bpPerPx),
-            _featureSpanPx4 = (0, _slicedToArray2.default)(_featureSpanPx3, 2),
-            _leftPx = _featureSpanPx4[0],
-            _rightPx = _featureSpanPx4[1];
-
-        var _score = _feature.get('score');
-
-        var snpinfo = _feature.get('snpinfo');
-
-        var _w = Math.max(_rightPx - _leftPx + 0.3, 1);
-
-        var totalScore = snpinfo.total;
-        var keys = Object.keys(snpinfo.cov).sort();
-        var curr = 0;
-
-        for (var _i2 = 0; _i2 < keys.length; _i2++) {
-          var base = keys[_i2];
-          var total = snpinfo.cov[base].total;
-          ctx.fillStyle = colorForBase[base] || modificationTagMap[base.replace('mod_', '')] || '#888';
-
-          var _height = toHeight(_score);
-
-          var bottom = toY(_score) + _height;
-
-          ctx.fillRect(_leftPx, bottom - (total + curr) / _score * _height, _w, total / _score * _height);
-          curr += total;
-        }
-
-        var interbaseEvents = Object.keys(snpinfo.noncov);
-        var indicatorHeight = 4.5;
-
-        if (drawInterbaseCounts) {
-          var _curr = 0;
-
-          for (var _i3 = 0; _i3 < interbaseEvents.length; _i3++) {
-            var _base = interbaseEvents[_i3];
-            var _total = snpinfo.noncov[_base].total;
-            ctx.fillStyle = colorForBase[_base];
-            ctx.fillRect(_leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(_curr), 1.2, indicatorToHeight(_total));
-            _curr += _total;
-          }
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
         }
-
-        if (drawIndicators) {
-          var accum = 0;
-          var max = 0;
-          var maxBase = '';
-
-          for (var _i4 = 0; _i4 < interbaseEvents.length; _i4++) {
-            var _base2 = interbaseEvents[_i4];
-            var _total2 = snpinfo.noncov[_base2].total;
-            accum += _total2;
-
-            if (_total2 > max) {
-              max = _total2;
-              maxBase = _base2;
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          } // avoid drawing a bunch of indicators if coverage is very low e.g.
-          // less than 7, uses the prev total in the case of the "cliff"
-
-
-          var indicatorComparatorScore = Math.max(totalScore, prevTotal);
-
-          if (accum > indicatorComparatorScore * indicatorThreshold && indicatorComparatorScore > 7) {
-            ctx.fillStyle = colorForBase[maxBase];
-            ctx.beginPath();
-            var l = _leftPx + extraHorizontallyFlippedOffset;
-            ctx.moveTo(l - 3.5, 0);
-            ctx.lineTo(l + 3.5, 0);
-            ctx.lineTo(l, indicatorHeight);
-            ctx.fill();
-          }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
         }
-
-        prevTotal = totalScore;
-      }
-
-      if (drawArcs) {
-        for (var _i5 = 0; _i5 < skips.length; _i5++) {
-          var f = skips[_i5];
-
-          var _bpSpanPx = (0, _util.bpSpanPx)(f.get('start'), f.get('end'), region, bpPerPx),
-              _bpSpanPx2 = (0, _slicedToArray2.default)(_bpSpanPx, 2),
-              left = _bpSpanPx2[0],
-              right = _bpSpanPx2[1];
-
-          ctx.beginPath();
-          var str = f.get('strand');
-          var xs = f.get('xs');
-          var pos = 'rgba(255,200,200,0.7)';
-          var neg = 'rgba(200,200,255,0.7)';
-          var neutral = 'rgba(200,200,200,0.7)';
-
-          if (xs === '+') {
-            ctx.strokeStyle = pos;
-          } else if (xs === '-') {
-            ctx.strokeStyle = neg;
-          } else if (str === 1) {
-            ctx.strokeStyle = pos;
-          } else if (str === -1) {
-            ctx.strokeStyle = neg;
-          } else {
-            ctx.strokeStyle = neutral;
-          }
-
-          ctx.lineWidth = Math.log(f.get('score') + 1);
-          ctx.moveTo(left, height - offset * 2);
-          ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
-          ctx.stroke();
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
         }
-      }
-
-      if (displayCrossHatches) {
-        ctx.lineWidth = 1;
-        ctx.strokeStyle = 'rgba(140,140,140,0.8)';
-        ticks.values.forEach(function (tick) {
-          ctx.beginPath();
-          ctx.moveTo(0, Math.round(toY(tick)));
-          ctx.lineTo(width, Math.round(toY(tick)));
-          ctx.stroke();
-        });
-      }
     }
-  }]);
-  return SNPCoverageRenderer;
-}(_pluginWiggle.WiggleBaseRenderer);
-
-exports.default = SNPCoverageRenderer;
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var ui_1 = require("@jbrowse/core/ui");
+var util_1 = require("@jbrowse/core/util");
+var configuration_1 = require("@jbrowse/core/configuration");
+var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+var SNPCoverageRenderer = /** @class */ (function (_super) {
+    __extends(SNPCoverageRenderer, _super);
+    function SNPCoverageRenderer() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    // note: the snps are drawn on linear scale even if the data is drawn in log
+    // scape hence the two different scales being used
+    SNPCoverageRenderer.prototype.draw = function (ctx, props) {
+        return __awaiter(this, void 0, void 0, function () {
+            var features, regions, bpPerPx, displayCrossHatches, _a, modificationTagMap, scaleOpts, unadjustedHeight, configTheme, cfg, ticks, theme, _b, region, width, offset, height, domain, opts, viewScale, indicatorViewScale, originY, indicatorThreshold, drawInterbaseCounts, drawArcs, drawIndicators, toY, toHeight, indicatorToY, indicatorToHeight, bases, colorForBase, feats, coverage, skips, i, feature, _c, leftPx, rightPx, w, score, prevTotal, extraHorizontallyFlippedOffset, i, feature, _d, leftPx, rightPx, score, snpinfo, w, totalScore, keys, curr, i_1, base, total, height_1, bottom, interbaseEvents, indicatorHeight, curr_1, i_2, base, total, accum, max, maxBase, i_3, base, total, indicatorComparatorScore, l, i, f, _e, left, right, str, xs, pos, neg, neutral;
+            return __generator(this, function (_f) {
+                features = props.features, regions = props.regions, bpPerPx = props.bpPerPx, displayCrossHatches = props.displayCrossHatches, _a = props.modificationTagMap, modificationTagMap = _a === void 0 ? {} : _a, scaleOpts = props.scaleOpts, unadjustedHeight = props.height, configTheme = props.theme, cfg = props.config, ticks = props.ticks;
+                theme = (0, ui_1.createJBrowseTheme)(configTheme);
+                _b = __read(regions, 1), region = _b[0];
+                width = (region.end - region.start) / bpPerPx;
+                offset = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
+                height = unadjustedHeight - offset * 2;
+                domain = scaleOpts.domain;
+                if (!domain) {
+                    return [2 /*return*/];
+                }
+                opts = __assign(__assign({}, scaleOpts), { range: [0, height] });
+                viewScale = (0, plugin_wiggle_1.getScale)(opts);
+                indicatorViewScale = (0, plugin_wiggle_1.getScale)(__assign(__assign({}, opts), { range: [0, height / 2], scaleType: 'linear' }));
+                originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
+                indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
+                drawInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'drawInterbaseCounts');
+                drawArcs = (0, configuration_1.readConfObject)(cfg, 'drawArcs');
+                drawIndicators = (0, configuration_1.readConfObject)(cfg, 'drawIndicators');
+                toY = function (n) { return height - (viewScale(n) || 0) + offset; };
+                toHeight = function (n) { return toY(originY) - toY(n); };
+                indicatorToY = function (n) {
+                    return height - (indicatorViewScale(n) || 0) + offset;
+                };
+                indicatorToHeight = function (n) {
+                    return indicatorToY((0, plugin_wiggle_1.getOrigin)('linear')) - indicatorToY(n);
+                };
+                bases = theme.palette.bases;
+                colorForBase = {
+                    A: bases.A.main,
+                    C: bases.C.main,
+                    G: bases.G.main,
+                    T: bases.T.main,
+                    total: 'lightgrey',
+                    insertion: 'purple',
+                    softclip: 'blue',
+                    hardclip: 'red',
+                    meth: 'red',
+                    unmeth: 'blue',
+                    ref: 'lightgrey',
+                };
+                feats = __spreadArray([], __read(features.values()), false);
+                coverage = feats.filter(function (f) { return f.get('type') !== 'skip'; });
+                skips = feats.filter(function (f) { return f.get('type') === 'skip'; });
+                // Use two pass rendering, which helps in visualizing the SNPs at higher
+                // bpPerPx First pass: draw the gray background
+                ctx.fillStyle = colorForBase.total;
+                for (i = 0; i < coverage.length; i++) {
+                    feature = coverage[i];
+                    _c = __read((0, util_1.featureSpanPx)(feature, region, bpPerPx), 2), leftPx = _c[0], rightPx = _c[1];
+                    w = rightPx - leftPx + 0.3;
+                    score = feature.get('score');
+                    ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+                }
+                prevTotal = 0;
+                extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
+                // Second pass: draw the SNP data, and add a minimum feature width of 1px
+                // which can be wider than the actual bpPerPx This reduces overdrawing of
+                // the grey background over the SNPs
+                for (i = 0; i < coverage.length; i++) {
+                    feature = coverage[i];
+                    _d = __read((0, util_1.featureSpanPx)(feature, region, bpPerPx), 2), leftPx = _d[0], rightPx = _d[1];
+                    score = feature.get('score');
+                    snpinfo = feature.get('snpinfo');
+                    w = Math.max(rightPx - leftPx + 0.3, 1);
+                    totalScore = snpinfo.total;
+                    keys = Object.keys(snpinfo.cov).sort();
+                    curr = 0;
+                    for (i_1 = 0; i_1 < keys.length; i_1++) {
+                        base = keys[i_1];
+                        total = snpinfo.cov[base].total;
+                        ctx.fillStyle =
+                            colorForBase[base] ||
+                                modificationTagMap[base.replace('mod_', '')] ||
+                                '#888';
+                        height_1 = toHeight(score);
+                        bottom = toY(score) + height_1;
+                        ctx.fillRect(leftPx, bottom - ((total + curr) / score) * height_1, w, (total / score) * height_1);
+                        curr += total;
+                    }
+                    interbaseEvents = Object.keys(snpinfo.noncov);
+                    indicatorHeight = 4.5;
+                    if (drawInterbaseCounts) {
+                        curr_1 = 0;
+                        for (i_2 = 0; i_2 < interbaseEvents.length; i_2++) {
+                            base = interbaseEvents[i_2];
+                            total = snpinfo.noncov[base].total;
+                            ctx.fillStyle = colorForBase[base];
+                            ctx.fillRect(leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(curr_1), 1.2, indicatorToHeight(total));
+                            curr_1 += total;
+                        }
+                    }
+                    if (drawIndicators) {
+                        accum = 0;
+                        max = 0;
+                        maxBase = '';
+                        for (i_3 = 0; i_3 < interbaseEvents.length; i_3++) {
+                            base = interbaseEvents[i_3];
+                            total = snpinfo.noncov[base].total;
+                            accum += total;
+                            if (total > max) {
+                                max = total;
+                                maxBase = base;
+                            }
+                        }
+                        indicatorComparatorScore = Math.max(totalScore, prevTotal);
+                        if (accum > indicatorComparatorScore * indicatorThreshold &&
+                            indicatorComparatorScore > 7) {
+                            ctx.fillStyle = colorForBase[maxBase];
+                            ctx.beginPath();
+                            l = leftPx + extraHorizontallyFlippedOffset;
+                            ctx.moveTo(l - 3.5, 0);
+                            ctx.lineTo(l + 3.5, 0);
+                            ctx.lineTo(l, indicatorHeight);
+                            ctx.fill();
+                        }
+                    }
+                    prevTotal = totalScore;
+                }
+                if (drawArcs) {
+                    for (i = 0; i < skips.length; i++) {
+                        f = skips[i];
+                        _e = __read((0, util_1.bpSpanPx)(f.get('start'), f.get('end'), region, bpPerPx), 2), left = _e[0], right = _e[1];
+                        ctx.beginPath();
+                        str = f.get('strand');
+                        xs = f.get('xs');
+                        pos = 'rgba(255,200,200,0.7)';
+                        neg = 'rgba(200,200,255,0.7)';
+                        neutral = 'rgba(200,200,200,0.7)';
+                        if (xs === '+') {
+                            ctx.strokeStyle = pos;
+                        }
+                        else if (xs === '-') {
+                            ctx.strokeStyle = neg;
+                        }
+                        else if (str === 1) {
+                            ctx.strokeStyle = pos;
+                        }
+                        else if (str === -1) {
+                            ctx.strokeStyle = neg;
+                        }
+                        else {
+                            ctx.strokeStyle = neutral;
+                        }
+                        ctx.lineWidth = Math.log(f.get('score') + 1);
+                        ctx.moveTo(left, height - offset * 2);
+                        ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
+                        ctx.stroke();
+                    }
+                }
+                if (displayCrossHatches) {
+                    ctx.lineWidth = 1;
+                    ctx.strokeStyle = 'rgba(140,140,140,0.8)';
+                    ticks.values.forEach(function (tick) {
+                        ctx.beginPath();
+                        ctx.moveTo(0, Math.round(toY(tick)));
+                        ctx.lineTo(width, Math.round(toY(tick)));
+                        ctx.stroke();
+                    });
+                }
+                return [2 /*return*/];
+            });
+        });
+    };
+    return SNPCoverageRenderer;
+}(plugin_wiggle_1.WiggleBaseRenderer));
+exports.default = SNPCoverageRenderer;
+//# sourceMappingURL=SNPCoverageRenderer.js.map

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -0,0 +1 @@
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package/dist/SNPCoverageRenderer/configSchema.js

@@ -1,40 +1,31 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {
-  clipColor: {
-    type: 'color',
-    description: 'the color of the clipping marker',
-    defaultValue: 'red'
-  },
-  indicatorThreshold: {
-    type: 'number',
-    description: 'the proportion of reads containing a insertion/clip indicator',
-    defaultValue: 0.4
-  },
-  drawArcs: {
-    type: 'boolean',
-    description: 'Draw sashimi-style arcs for intron features',
-    defaultValue: true
-  },
-  drawInterbaseCounts: {
-    type: 'boolean',
-    description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
-    defaultValue: true
-  },
-  drawIndicators: {
-    type: 'boolean',
-    description: 'draw a triangular indicator where an event has been detected',
-    defaultValue: true
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {
+    clipColor: {
+        type: 'color',
+        description: 'the color of the clipping marker',
+        defaultValue: 'red',
+    },
+    indicatorThreshold: {
+        type: 'number',
+        description: 'the proportion of reads containing a insertion/clip indicator',
+        defaultValue: 0.4,
+    },
+    drawArcs: {
+        type: 'boolean',
+        description: 'Draw sashimi-style arcs for intron features',
+        defaultValue: true,
+    },
+    drawInterbaseCounts: {
+        type: 'boolean',
+        description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
+        defaultValue: true,
+    },
+    drawIndicators: {
+        type: 'boolean',
+        description: 'draw a triangular indicator where an event has been detected',
+        defaultValue: true,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageRenderer/configSchema.js.map

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