@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/components/PileupRendering.js

@@ -1,15 +1,4 @@
 "use strict";
-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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -33,56 +22,40 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-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;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importStar(require("react"));
-var ui_1 = require("@jbrowse/core/ui");
-var util_1 = require("@jbrowse/core/util");
-var mobx_react_1 = require("mobx-react");
+const react_1 = __importStar(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
 // used so that user can click-away-from-feature below the laid out features
 // (issue #1248)
-var canvasPadding = 100;
+const canvasPadding = 100;
 function PileupRendering(props) {
-    var onMouseMove = props.onMouseMove, blockKey = props.blockKey, displayModel = props.displayModel, width = props.width, height = props.height, regions = props.regions, bpPerPx = props.bpPerPx, sortedBy = props.sortedBy, colorBy = props.colorBy;
-    var selectedFeatureId = displayModel.selectedFeatureId, featureIdUnderMouse = displayModel.featureIdUnderMouse, contextMenuFeature = displayModel.contextMenuFeature;
-    var _a = __read(regions, 1), region = _a[0];
-    var highlightOverlayCanvas = (0, react_1.useRef)(null);
-    var _b = __read((0, react_1.useState)(false), 2), mouseIsDown = _b[0], setMouseIsDown = _b[1];
-    var _c = __read((0, react_1.useState)(false), 2), movedDuringLastMouseDown = _c[0], setMovedDuringLastMouseDown = _c[1];
-    (0, react_1.useEffect)(function () {
+    const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, } = props;
+    const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } = displayModel;
+    const [region] = regions;
+    const highlightOverlayCanvas = (0, react_1.useRef)(null);
+    const [mouseIsDown, setMouseIsDown] = (0, react_1.useState)(false);
+    const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] = (0, react_1.useState)(false);
+    (0, react_1.useEffect)(() => {
         var _a, _b;
-        var canvas = highlightOverlayCanvas.current;
+        const canvas = highlightOverlayCanvas.current;
         if (!canvas) {
             return;
         }
-        var ctx = canvas.getContext('2d');
+        const ctx = canvas.getContext('2d');
         if (!ctx) {
             return;
         }
         ctx.clearRect(0, 0, canvas.width, canvas.height);
-        var selectedRect = selectedFeatureId
+        const selectedRect = selectedFeatureId
             ? (_a = displayModel.getFeatureByID) === null || _a === void 0 ? void 0 : _a.call(displayModel, blockKey, selectedFeatureId)
             : undefined;
         if (selectedRect) {
-            var _c = __read(selectedRect, 4), leftBp = _c[0], topPx = _c[1], rightBp = _c[2], bottomPx = _c[3];
-            var _d = __read((0, util_1.bpSpanPx)(leftBp, rightBp, region, bpPerPx), 2), leftPx = _d[0], rightPx = _d[1];
-            var rectTop = Math.round(topPx);
-            var rectHeight = Math.round(bottomPx - topPx);
+            const [leftBp, topPx, rightBp, bottomPx] = selectedRect;
+            const [leftPx, rightPx] = (0, util_1.bpSpanPx)(leftBp, rightBp, region, bpPerPx);
+            const rectTop = Math.round(topPx);
+            const rectHeight = Math.round(bottomPx - topPx);
             ctx.shadowColor = '#222266';
             ctx.shadowBlur = 10;
             ctx.lineJoin = 'bevel';
@@ -91,15 +64,15 @@ function PileupRendering(props) {
             ctx.strokeRect(leftPx - 2, rectTop - 2, rightPx - leftPx + 4, rectHeight + 4);
             ctx.clearRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
         }
-        var highlightedFeature = featureIdUnderMouse || (contextMenuFeature === null || contextMenuFeature === void 0 ? void 0 : contextMenuFeature.id());
-        var highlightedRect = highlightedFeature
+        const highlightedFeature = featureIdUnderMouse || (contextMenuFeature === null || contextMenuFeature === void 0 ? void 0 : contextMenuFeature.id());
+        const highlightedRect = highlightedFeature
             ? (_b = displayModel.getFeatureByID) === null || _b === void 0 ? void 0 : _b.call(displayModel, blockKey, highlightedFeature)
             : undefined;
         if (highlightedRect) {
-            var _e = __read(highlightedRect, 4), leftBp = _e[0], topPx = _e[1], rightBp = _e[2], bottomPx = _e[3];
-            var _f = __read((0, util_1.bpSpanPx)(leftBp, rightBp, region, bpPerPx), 2), leftPx = _f[0], rightPx = _f[1];
-            var rectTop = Math.round(topPx);
-            var rectHeight = Math.round(bottomPx - topPx);
+            const [leftBp, topPx, rightBp, bottomPx] = highlightedRect;
+            const [leftPx, rightPx] = (0, util_1.bpSpanPx)(leftBp, rightBp, region, bpPerPx);
+            const rectTop = Math.round(topPx);
+            const rectHeight = Math.round(bottomPx - topPx);
             ctx.fillStyle = '#0003';
             ctx.fillRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
         }
@@ -147,19 +120,19 @@ function PileupRendering(props) {
         if (mouseIsDown) {
             setMovedDuringLastMouseDown(true);
         }
-        var offsetX = 0;
-        var offsetY = 0;
-        var canvas = highlightOverlayCanvas.current;
+        let offsetX = 0;
+        let offsetY = 0;
+        const canvas = highlightOverlayCanvas.current;
         if (canvas) {
-            var _a = canvas.getBoundingClientRect(), left = _a.left, top_1 = _a.top;
+            const { left, top } = canvas.getBoundingClientRect();
             offsetX = left;
-            offsetY = top_1;
+            offsetY = top;
         }
         offsetX = event.clientX - offsetX;
         offsetY = event.clientY - offsetY;
-        var px = region.reversed ? width - offsetX : offsetX;
-        var clientBp = region.start + bpPerPx * px;
-        var featIdUnderMouse = displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY);
+        const px = region.reversed ? width - offsetX : offsetX;
+        const clientBp = region.start + bpPerPx * px;
+        const featIdUnderMouse = displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY);
         if (onMouseMove) {
             onMouseMove(event, featIdUnderMouse);
         }
@@ -167,10 +140,10 @@ function PileupRendering(props) {
     function callMouseHandler(handlerName, event) {
         // @ts-ignore
         // eslint-disable-next-line react/destructuring-assignment
-        var featureHandler = props["onFeature".concat(handlerName)];
+        const featureHandler = props[`onFeature${handlerName}`];
         // @ts-ignore
         // eslint-disable-next-line react/destructuring-assignment
-        var canvasHandler = props["on".concat(handlerName)];
+        const canvasHandler = props[`on${handlerName}`];
         if (featureHandler && featureIdUnderMouse) {
             featureHandler(event, featureIdUnderMouse);
         }
@@ -178,13 +151,13 @@ function PileupRendering(props) {
             canvasHandler(event, featureIdUnderMouse);
         }
     }
-    var canvasWidth = Math.ceil(width);
+    const canvasWidth = Math.ceil(width);
     // need to call this in render so we get the right observer behavior
-    return (react_1.default.createElement("div", { className: "PileupRendering", "data-testid": "pileup-".concat(sortedBy || colorBy
-            ? "".concat((sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) || '').concat((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || '').concat((colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) || '')
-            : 'normal'), style: { position: 'relative', width: canvasWidth, height: height } },
-        react_1.default.createElement(ui_1.PrerenderedCanvas, __assign({}, props, { style: { position: 'absolute', left: 0, top: 0 } })),
-        react_1.default.createElement("canvas", { "data-testid": "pileup_overlay_canvas", width: canvasWidth, height: height + canvasPadding, style: { position: 'absolute', left: 0, top: 0 }, className: "highlightOverlayCanvas", ref: highlightOverlayCanvas, onMouseDown: function (event) { return onMouseDown(event); }, onMouseEnter: function (event) { return onMouseEnter(event); }, onMouseOut: function (event) { return onMouseOut(event); }, onMouseOver: function (event) { return onMouseOver(event); }, onMouseUp: function (event) { return onMouseUp(event); }, onMouseLeave: function (event) { return onMouseLeave(event); }, onMouseMove: function (event) { return mouseMove(event); }, onClick: function (event) { return onClick(event); }, onContextMenu: function (event) { return onContextMenu(event); }, onFocus: function () { }, onBlur: function () { } })));
+    return (react_1.default.createElement("div", { className: "PileupRendering", "data-testid": `pileup-${sortedBy || colorBy
+            ? `${(sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) || ''}`
+            : 'normal'}`, style: { position: 'relative', width: canvasWidth, height } },
+        react_1.default.createElement(ui_1.PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }),
+        react_1.default.createElement("canvas", { "data-testid": "pileup_overlay_canvas", width: canvasWidth, height: height + canvasPadding, style: { position: 'absolute', left: 0, top: 0 }, className: "highlightOverlayCanvas", ref: highlightOverlayCanvas, onMouseDown: event => onMouseDown(event), onMouseEnter: event => onMouseEnter(event), onMouseOut: event => onMouseOut(event), onMouseOver: event => onMouseOver(event), onMouseUp: event => onMouseUp(event), onMouseLeave: event => onMouseLeave(event), onMouseMove: event => mouseMove(event), onClick: event => onClick(event), onContextMenu: event => onContextMenu(event), onFocus: () => { }, onBlur: () => { } })));
 }
 exports.default = (0, mobx_react_1.observer)(PileupRendering);
 //# sourceMappingURL=PileupRendering.js.map

package/dist/PileupRenderer/components/PileupRendering.js.map

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package/dist/PileupRenderer/configSchema.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
 exports.default = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
     // default magenta here is used to detect the user has not customized this
     color: {

package/dist/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,mDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,gBAAgB,EAChB;IACE,0EAA0E;IAC1E,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,mIAAmI;KACtI;IACD,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,gBAAgB,EAChB;IACE,0EAA0E;IAC1E,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,mIAAmI;KACtI;IACD,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/PileupRenderer/index.js

@@ -3,18 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
-var PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
-var configSchema_1 = __importDefault(require("./configSchema"));
+const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
+const PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 function register(pluginManager) {
-    pluginManager.addRendererType(function () {
-        return new PileupRenderer_1.default({
-            name: 'PileupRenderer',
-            ReactComponent: PileupRendering_1.default,
-            configSchema: configSchema_1.default,
-            pluginManager: pluginManager,
-        });
-    });
+    pluginManager.addRendererType(() => new PileupRenderer_1.default({
+        name: 'PileupRenderer',
+        ReactComponent: PileupRendering_1.default,
+        configSchema: configSchema_1.default,
+        pluginManager,
+    }));
 }
 exports.default = register;
 //# sourceMappingURL=index.js.map

package/dist/PileupRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,wBAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc,EAAd,yBAAc;QACd,YAAY,EAAZ,sBAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}

package/dist/PileupRenderer/sortUtil.js

@@ -1,17 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sortFeature = void 0;
-var range_1 = require("@jbrowse/core/util/range");
-var sortFeature = function (features, sortedBy) {
-    var featureArray = Array.from(features.values());
-    var featuresInCenterLine = [];
-    var featuresOutsideCenter = [];
-    var pos = sortedBy.pos, type = sortedBy.type;
+const range_1 = require("@jbrowse/core/util/range");
+const sortFeature = (features, sortedBy) => {
+    const featureArray = Array.from(features.values());
+    const featuresInCenterLine = [];
+    const featuresOutsideCenter = [];
+    const { pos, type } = sortedBy;
     // only sort on features that intersect center line, append those outside post-sort
-    featureArray.forEach(function (innerArray) {
-        var feature = innerArray;
-        var start = feature.get('start');
-        var end = feature.get('end');
+    featureArray.forEach(innerArray => {
+        const feature = innerArray;
+        const start = feature.get('start');
+        const end = feature.get('end');
         if ((0, range_1.doesIntersect2)(pos - 1, pos, start, end)) {
             featuresInCenterLine.push(innerArray);
         }
@@ -19,50 +19,48 @@ var sortFeature = function (features, sortedBy) {
             featuresOutsideCenter.push(innerArray);
         }
     });
-    var isCram = featureArray.length ? featureArray[0].get('tags') : false;
+    const isCram = featureArray.length ? featureArray[0].get('tags') : false;
     switch (type) {
         case 'Start location': {
-            featuresInCenterLine.sort(function (a, b) { return a.get('start') - b.get('start'); });
+            featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'));
             break;
         }
         case 'tag': {
-            var tag_1 = sortedBy.tag;
-            var getTag_1 = function (f, t) {
+            const tag = sortedBy.tag;
+            const getTag = (f, t) => {
                 return isCram ? f.get('tags')[t] : f.get(t);
             };
-            var isString = featuresInCenterLine[0] &&
-                typeof getTag_1(featuresInCenterLine[0], tag_1) === 'string';
+            const isString = featuresInCenterLine[0] &&
+                typeof getTag(featuresInCenterLine[0], tag) === 'string';
             if (isString) {
-                featuresInCenterLine.sort(function (a, b) {
-                    return getTag_1(b, tag_1).localeCompare(getTag_1(a, tag_1));
-                });
+                featuresInCenterLine.sort((a, b) => getTag(b, tag).localeCompare(getTag(a, tag)));
             }
             else {
-                featuresInCenterLine.sort(function (a, b) { return (getTag_1(b, tag_1) || 0) - (getTag_1(a, tag_1) || 0); });
+                featuresInCenterLine.sort((a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0));
             }
             break;
         }
         // first sort all mismatches, then all reference bases at the end
         case 'Base pair': {
-            var baseSortArray_1 = [];
-            featuresInCenterLine.forEach(function (feature) {
-                var mismatches = feature.get('mismatches');
-                mismatches.forEach(function (mismatch) {
-                    var start = feature.get('start');
-                    var offset = start + mismatch.start + 1;
-                    var consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
-                    var len = consuming ? 0 : mismatch.length;
+            const baseSortArray = [];
+            featuresInCenterLine.forEach(feature => {
+                const mismatches = feature.get('mismatches');
+                mismatches.forEach(mismatch => {
+                    const start = feature.get('start');
+                    const offset = start + mismatch.start + 1;
+                    const consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
+                    const len = consuming ? 0 : mismatch.length;
                     if (pos >= offset && pos < offset + len) {
-                        baseSortArray_1.push([feature.id(), mismatch]);
+                        baseSortArray.push([feature.id(), mismatch]);
                     }
                 });
             });
-            var baseMap_1 = new Map(baseSortArray_1);
-            featuresInCenterLine.sort(function (a, b) {
-                var aMismatch = baseMap_1.get(a.id());
-                var bMismatch = baseMap_1.get(b.id());
-                var acode = bMismatch && bMismatch.base.toUpperCase();
-                var bcode = aMismatch && aMismatch.base.toUpperCase();
+            const baseMap = new Map(baseSortArray);
+            featuresInCenterLine.sort((a, b) => {
+                const aMismatch = baseMap.get(a.id());
+                const bMismatch = baseMap.get(b.id());
+                const acode = bMismatch && bMismatch.base.toUpperCase();
+                const bcode = aMismatch && aMismatch.base.toUpperCase();
                 if (acode === bcode && acode === '*') {
                     // @ts-ignore
                     return aMismatch.length - bMismatch.length;
@@ -73,15 +71,13 @@ var sortFeature = function (features, sortedBy) {
         }
         // sorts positive strands then negative strands
         case 'Read strand': {
-            featuresInCenterLine.sort(function (a, b) {
-                return a.get('strand') <= b.get('strand') ? 1 : -1;
-            });
+            featuresInCenterLine.sort((a, b) => a.get('strand') <= b.get('strand') ? 1 : -1);
             break;
         }
     }
-    var sortedMap = new Map(featuresInCenterLine
+    const sortedMap = new Map(featuresInCenterLine
         .concat(featuresOutsideCenter)
-        .map(function (feature) { return [feature.id(), feature]; }));
+        .map(feature => [feature.id(), feature]));
     return sortedMap;
 };
 exports.sortFeature = sortFeature;

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