@jbrowse/plugin-alignments 2.1.0 → 2.1.2

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -1 +1 @@
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package/dist/SNPCoverageAdapter/configSchema.js

@@ -1,12 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = (function (pluginManager) {
-    return mobx_state_tree_1.types.late(function () {
-        return (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
-            subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        }, { explicitlyTyped: true });
-    });
-});
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (pluginManager) => mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
+    subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
+}, { explicitlyTyped: true }));
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,mDAAuC;AAEvC,mBAAe,UAAC,aAA4B;IAC1C,OAAA,uBAAK,CAAC,IAAI,CAAC;QACT,OAAA,IAAA,mCAAmB,EACjB,oBAAoB,EACpB;YACE,UAAU,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;SAC/D,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B;IAND,CAMC,CACF;AARD,CAQC,EAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,qDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE,CAC9C,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACd,IAAA,mCAAmB,EACjB,oBAAoB,EACpB;IACE,UAAU,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;CAC/D,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}

package/dist/SNPCoverageAdapter/index.js

@@ -26,25 +26,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var configSchema_1 = __importDefault(require("./configSchema"));
-var SNPCoverageAdapter_1 = require("./SNPCoverageAdapter");
-exports.default = (function (pluginManager) {
-    pluginManager.addAdapterType(function () {
-        return new AdapterType_1.default({
-            name: 'SNPCoverageAdapter',
-            adapterMetadata: {
-                category: null,
-                displayName: null,
-                hiddenFromGUI: true,
-                description: null,
-            },
-            getAdapterClass: function () {
-                return Promise.resolve().then(function () { return __importStar(require('./SNPCoverageAdapter')); }).then(function (r) { return r.default; });
-            },
-            configSchema: (0, configSchema_1.default)(pluginManager),
-            adapterCapabilities: SNPCoverageAdapter_1.capabilities,
-        });
-    });
-});
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+const SNPCoverageAdapter_1 = require("./SNPCoverageAdapter");
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'SNPCoverageAdapter',
+        adapterMetadata: {
+            category: null,
+            displayName: null,
+            hiddenFromGUI: true,
+            description: null,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
+        configSchema: (0, configSchema_1.default)(pluginManager),
+        adapterCapabilities: SNPCoverageAdapter_1.capabilities,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAgD;AAChD,6DAAmD;AAEnD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,oBAAoB;QAC1B,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,WAAW,EAAE,IAAI;YACjB,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;SAClB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,sBAAsB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,YAAY,EAAE,IAAA,sBAAmB,EAAC,aAAa,CAAC;QAChD,mBAAmB,EAAE,iCAAY;KAClC,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,271 +1,187 @@
 "use strict";
-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];
-        }
-        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;
-            }
-            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);
-        }
-        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];
-        }
-    }
-    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;
-    }
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
     // 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));
+    async draw(ctx, props) {
+        const { features, regions, bpPerPx, displayCrossHatches, modificationTagMap = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, } = props;
+        const theme = (0, ui_1.createJBrowseTheme)(configTheme);
+        const [region] = regions;
+        const 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
+        const offset = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
+        const height = unadjustedHeight - offset * 2;
+        const { domain } = scaleOpts;
+        if (!domain) {
+            return;
+        }
+        const opts = { ...scaleOpts, range: [0, height] };
+        const viewScale = (0, plugin_wiggle_1.getScale)(opts);
+        // clipping and insertion indicators, uses a smaller height/2 scale
+        const indicatorViewScale = (0, plugin_wiggle_1.getScale)({
+            ...opts,
+            range: [0, height / 2],
+            scaleType: 'linear',
+        });
+        const originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
+        const indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
+        const drawInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'drawInterbaseCounts');
+        const drawArcs = (0, configuration_1.readConfObject)(cfg, 'drawArcs');
+        const drawIndicators = (0, configuration_1.readConfObject)(cfg, 'drawIndicators');
+        // get the y coordinate that we are plotting at, this can be log scale
+        const toY = (n) => height - (viewScale(n) || 0) + offset;
+        const toHeight = (n) => toY(originY) - toY(n);
+        const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
+        const indicatorToHeight = (n) => indicatorToY((0, plugin_wiggle_1.getOrigin)('linear')) - indicatorToY(n);
+        const { bases } = theme.palette;
+        const 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',
+        };
+        const feats = [...features.values()];
+        const coverage = feats.filter(f => f.get('type') !== 'skip');
+        const skips = feats.filter(f => 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 (let i = 0; i < coverage.length; i++) {
+            const feature = coverage[i];
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            const w = rightPx - leftPx + 0.3;
+            const 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"
+        let prevTotal = 0;
+        // extraHorizontallyFlippedOffset is used to draw interbase items, which
+        // are located to the left when forward and right when reversed
+        const 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 (let i = 0; i < coverage.length; i++) {
+            const feature = coverage[i];
+            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+            const score = feature.get('score');
+            const snpinfo = feature.get('snpinfo');
+            const w = Math.max(rightPx - leftPx + 0.3, 1);
+            const totalScore = snpinfo.total;
+            const keys = Object.keys(snpinfo.cov).sort();
+            let curr = 0;
+            for (let i = 0; i < keys.length; i++) {
+                const base = keys[i];
+                const { total } = snpinfo.cov[base];
+                ctx.fillStyle =
+                    colorForBase[base] ||
+                        modificationTagMap[base.replace('mod_', '')] ||
+                        '#888';
+                const height = toHeight(score);
+                const bottom = toY(score) + height;
+                ctx.fillRect(leftPx, bottom - ((total + curr) / score) * height, w, (total / score) * height);
+                curr += total;
+            }
+            const interbaseEvents = Object.keys(snpinfo.noncov);
+            const indicatorHeight = 4.5;
+            if (drawInterbaseCounts) {
+                let curr = 0;
+                for (let i = 0; i < interbaseEvents.length; i++) {
+                    const base = interbaseEvents[i];
+                    const { total } = snpinfo.noncov[base];
+                    ctx.fillStyle = colorForBase[base];
+                    ctx.fillRect(leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(curr), 1.2, indicatorToHeight(total));
+                    curr += total;
                 }
-                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();
-                        }
+            }
+            if (drawIndicators) {
+                let accum = 0;
+                let max = 0;
+                let maxBase = '';
+                for (let i = 0; i < interbaseEvents.length; i++) {
+                    const base = interbaseEvents[i];
+                    const { total } = snpinfo.noncov[base];
+                    accum += total;
+                    if (total > max) {
+                        max = total;
+                        maxBase = base;
                     }
-                    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();
-                    }
+                // 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"
+                const indicatorComparatorScore = Math.max(totalScore, prevTotal);
+                if (accum > indicatorComparatorScore * indicatorThreshold &&
+                    indicatorComparatorScore > 7) {
+                    ctx.fillStyle = colorForBase[maxBase];
+                    ctx.beginPath();
+                    const 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 (let i = 0; i < skips.length; i++) {
+                const f = skips[i];
+                const [left, right] = (0, util_1.bpSpanPx)(f.get('start'), f.get('end'), region, bpPerPx);
+                ctx.beginPath();
+                const str = f.get('strand');
+                const xs = f.get('xs');
+                const pos = 'rgba(255,200,200,0.7)';
+                const neg = 'rgba(200,200,255,0.7)';
+                const neutral = 'rgba(200,200,200,0.7)';
+                if (xs === '+') {
+                    ctx.strokeStyle = pos;
+                }
+                else if (xs === '-') {
+                    ctx.strokeStyle = neg;
                 }
-                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();
-                    });
+                else if (str === 1) {
+                    ctx.strokeStyle = pos;
                 }
-                return [2 /*return*/];
+                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(tick => {
+                ctx.beginPath();
+                ctx.moveTo(0, Math.round(toY(tick)));
+                ctx.lineTo(width, Math.round(toY(tick)));
+                ctx.stroke();
             });
-        });
-    };
-    return SNPCoverageRenderer;
-}(plugin_wiggle_1.WiggleBaseRenderer));
+        }
+    }
+}
 exports.default = SNPCoverageRenderer;
 //# sourceMappingURL=SNPCoverageRenderer.js.map