@jbrowse/plugin-alignments 2.6.1 → 2.6.2

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -273,4 +273,3 @@ function stateModelFactory(pluginManager, configSchema) {
     });
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/MismatchParser/index.js

@@ -448,4 +448,3 @@ function featurizeSA(SA, id, strand, readName, normalize) {
     })) || []);
 }
 exports.featurizeSA = featurizeSA;
-//# sourceMappingURL=index.js.map

package/dist/PileupRPC/base.js

@@ -19,4 +19,3 @@ class PileupBaseRPC extends RpcMethodType_1.default {
     }
 }
 exports.default = PileupBaseRPC;
-//# sourceMappingURL=base.js.map

package/dist/PileupRPC/index.js

@@ -6,4 +6,3 @@ exports.default = (pm) => {
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
 };
-//# sourceMappingURL=index.js.map

package/dist/PileupRPC/methods/GetGlobalValueForTag.js

@@ -28,4 +28,3 @@ class PileupGetGlobalValueForTag extends base_1.default {
     }
 }
 exports.default = PileupGetGlobalValueForTag;
-//# sourceMappingURL=GetGlobalValueForTag.js.map

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -49,4 +49,3 @@ class PileupGetReducedFeatures extends base_1.default {
     }
 }
 exports.default = PileupGetReducedFeatures;
-//# sourceMappingURL=GetReducedFeatures.js.map

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -27,4 +27,3 @@ class PileupGetVisibleModifications extends base_1.default {
     }
 }
 exports.default = PileupGetVisibleModifications;
-//# sourceMappingURL=GetVisibleModifications.js.map

package/dist/PileupRPC/rpcMethods.js

@@ -10,4 +10,3 @@ var GetVisibleModifications_1 = require("./methods/GetVisibleModifications");
 Object.defineProperty(exports, "PileupGetVisibleModifications", { enumerable: true, get: function () { return __importDefault(GetVisibleModifications_1).default; } });
 var GetGlobalValueForTag_1 = require("./methods/GetGlobalValueForTag");
 Object.defineProperty(exports, "PileupGetGlobalValueForTag", { enumerable: true, get: function () { return __importDefault(GetGlobalValueForTag_1).default; } });
-//# sourceMappingURL=rpcMethods.js.map

package/dist/PileupRPC/util.js

@@ -17,4 +17,3 @@ function filterForPairs(features) {
     return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
 }
 exports.filterForPairs = filterForPairs;
-//# sourceMappingURL=util.js.map

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -36,4 +36,3 @@ class PileupLayoutSession extends BoxRendererType_1.LayoutSession {
     }
 }
 exports.PileupLayoutSession = PileupLayoutSession;
-//# sourceMappingURL=PileupLayoutSession.js.map

package/dist/PileupRenderer/PileupRenderer.js

@@ -117,4 +117,3 @@ class PileupRenderer extends BoxRendererType_1.default {
     }
 }
 exports.default = PileupRenderer;
-//# sourceMappingURL=PileupRenderer.js.map

package/dist/PileupRenderer/colorBy.js

@@ -39,31 +39,32 @@ function getStranded(feature) {
     const strand = feature.get('strand');
     // is paired
     if (flags & 1) {
-        const revflag = flags & 64;
-        const flipper = revflag ? -1 : 1;
+        // first-of-pair?
+        const flipper = flags & 64 ? -1 : 1;
         // proper pairing
         if (flags & 2) {
             return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand';
         }
-        else if (feature.get('multi_segment_next_segment_unmapped')) {
+        // mate missing, separate color
+        else if (flags & 8) {
             return strand * flipper === 1
                 ? 'color_rev_missing_mate'
                 : 'color_fwd_missing_mate';
         }
-        else if (feature.get('refName') === feature.get('next_refName')) {
+        // same chrom without proper pairing gets separate color
+        else if (feature.get('refName') === feature.get('next_ref')) {
             return strand * flipper === 1
                 ? 'color_rev_strand_not_proper'
                 : 'color_fwd_strand_not_proper';
         }
+        // abberant chrom
         else {
-            // should only leave aberrant chr
             return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
         }
     }
-    return strand === 1 ? 'color_fwd_strand' : 'color_rev_strand';
+    return 'color_unknown';
 }
 function colorByStrandedRnaSeq(feature) {
     return color_1.fillColor[getStranded(feature)];
 }
 exports.colorByStrandedRnaSeq = colorByStrandedRnaSeq;
-//# sourceMappingURL=colorBy.js.map

package/dist/PileupRenderer/components/PileupRendering.js

@@ -159,4 +159,3 @@ function PileupRendering(props) {
         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/configSchema.js

@@ -98,4 +98,3 @@ const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer'
     },
 }, { explicitlyTyped: true });
 exports.default = PileupRenderer;
-//# sourceMappingURL=configSchema.js.map

package/dist/PileupRenderer/getAlignmentShapeColor.js

@@ -57,4 +57,3 @@ function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor,
     }
 }
 exports.getAlignmentShapeColor = getAlignmentShapeColor;
-//# sourceMappingURL=getAlignmentShapeColor.js.map

package/dist/PileupRenderer/index.js

@@ -18,4 +18,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/PileupRenderer/layoutFeature.js

@@ -38,4 +38,3 @@ function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightP
     };
 }
 exports.layoutFeature = layoutFeature;
-//# sourceMappingURL=layoutFeature.js.map

package/dist/PileupRenderer/layoutFeatures.js

@@ -32,4 +32,3 @@ function layoutFeats(props) {
     }), featureMap.size);
 }
 exports.layoutFeats = layoutFeats;
-//# sourceMappingURL=layoutFeatures.js.map

package/dist/PileupRenderer/makeImageData.js

@@ -61,4 +61,3 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     }
 }
 exports.makeImageData = makeImageData;
-//# sourceMappingURL=makeImageData.js.map

package/dist/PileupRenderer/renderAlignment.js

@@ -69,4 +69,3 @@ function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase,
     }
 }
 exports.renderAlignment = renderAlignment;
-//# sourceMappingURL=renderAlignment.js.map

package/dist/PileupRenderer/renderAlignmentShape.js

@@ -11,7 +11,7 @@ function renderAlignmentShape({ ctx, feat, renderArgs, }) {
     const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
     const flip = region.reversed ? -1 : 1;
     const strand = feature.get('strand') * flip;
-    if (bpPerPx < 10) {
+    if (bpPerPx < 10 && heightPx > 5) {
         if (strand === -1) {
             ctx.beginPath();
             ctx.moveTo(leftPx - 5, topPx + heightPx / 2);
@@ -38,4 +38,3 @@ function renderAlignmentShape({ ctx, feat, renderArgs, }) {
     }
 }
 exports.renderAlignmentShape = renderAlignmentShape;
-//# sourceMappingURL=renderAlignmentShape.js.map

package/dist/PileupRenderer/renderMethylation.js

@@ -60,4 +60,3 @@ function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth
     }
 }
 exports.renderMethylation = renderMethylation;
-//# sourceMappingURL=renderMethylation.js.map

package/dist/PileupRenderer/renderMismatches.js

@@ -132,4 +132,3 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
     }
 }
 exports.renderMismatches = renderMismatches;
-//# sourceMappingURL=renderMismatches.js.map

package/dist/PileupRenderer/renderModifications.js

@@ -51,4 +51,3 @@ function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWid
     }
 }
 exports.renderModifications = renderModifications;
-//# sourceMappingURL=renderModifications.js.map

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -44,4 +44,3 @@ function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, cont
     }
 }
 exports.renderPerBaseLettering = renderPerBaseLettering;
-//# sourceMappingURL=renderPerBaseLettering.js.map

package/dist/PileupRenderer/renderPerBaseQuality.js

@@ -36,4 +36,3 @@ function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
     }
 }
 exports.renderPerBaseQuality = renderPerBaseQuality;
-//# sourceMappingURL=renderPerBaseQuality.js.map

package/dist/PileupRenderer/renderSoftClipping.js

@@ -45,4 +45,3 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
     });
 }
 exports.renderSoftClipping = renderSoftClipping;
-//# sourceMappingURL=renderSoftClipping.js.map

package/dist/PileupRenderer/sortUtil.js

@@ -81,4 +81,3 @@ const sortFeature = (features, sortedBy) => {
     ]));
 };
 exports.sortFeature = sortFeature;
-//# sourceMappingURL=sortUtil.js.map

package/dist/PileupRenderer/util.js

@@ -48,4 +48,3 @@ function getCharWidthHeight() {
     return { charWidth, charHeight };
 }
 exports.getCharWidthHeight = getCharWidthHeight;
-//# sourceMappingURL=util.js.map

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -81,4 +81,3 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = SNPCoverageAdapter;
-//# sourceMappingURL=SNPCoverageAdapter.js.map

package/dist/SNPCoverageAdapter/configSchema.js

@@ -16,4 +16,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapte
     },
 }, { explicitlyTyped: true });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -209,4 +209,3 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
     return { bins, skipmap };
 }
 exports.default = generateCoverageBins;
-//# sourceMappingURL=generateCoverageBins.js.map

package/dist/SNPCoverageAdapter/index.js

@@ -42,4 +42,3 @@ function default_1(pluginManager) {
     });
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/dist/SNPCoverageAdapter/util.js

@@ -1,3 +1,2 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=util.js.map

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -187,4 +187,3 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
     }
 }
 exports.default = SNPCoverageRenderer;
-//# sourceMappingURL=SNPCoverageRenderer.js.map

package/dist/SNPCoverageRenderer/configSchema.js

@@ -53,4 +53,3 @@ const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverag
     },
 }, { explicitlyTyped: true });
 exports.default = SNPCoverageRenderer;
-//# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageRenderer/index.js

@@ -15,4 +15,3 @@ function register(pluginManager) {
     }));
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -74,4 +74,3 @@ var LinearPileupDisplay_2 = require("./LinearPileupDisplay");
 Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayStateModelFactory; } });
 Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayConfigSchemaFactory; } });
 exports.MismatchParser = __importStar(require("./MismatchParser"));
-//# sourceMappingURL=index.js.map

package/dist/shared/BaseDisplayComponent.js

@@ -46,4 +46,3 @@ const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement("div", { className: classes.loading },
         react_1.default.createElement(ui_1.LoadingEllipses, { message: message })));
 });
-//# sourceMappingURL=BaseDisplayComponent.js.map

package/dist/shared/FilterByTag.js

@@ -124,4 +124,3 @@ function FilterByTagDlg(props) {
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(FilterByTagDlg);
-//# sourceMappingURL=FilterByTag.js.map

package/dist/shared/afterAttach.js

@@ -41,4 +41,3 @@ function doAfterAttach(self, cb) {
     }, { delay: 1000 });
 }
 exports.doAfterAttach = doAfterAttach;
-//# sourceMappingURL=afterAttach.js.map

package/dist/shared/color.js

@@ -74,4 +74,3 @@ function getPairedOrientationColor(f) {
     ];
 }
 exports.getPairedOrientationColor = getPairedOrientationColor;
-//# sourceMappingURL=color.js.map

package/dist/shared/fetchChains.js

@@ -21,4 +21,3 @@ async function fetchChains(self) {
     self.setLoading(false);
 }
 exports.fetchChains = fetchChains;
-//# sourceMappingURL=fetchChains.js.map

package/dist/shared/index.js

@@ -40,4 +40,3 @@ exports.FilterModel = mobx_state_tree_1.types.model({
         value: mobx_state_tree_1.types.string,
     })),
 });
-//# sourceMappingURL=index.js.map

package/dist/shared/renderSvg.js

@@ -66,4 +66,3 @@ async function renderSvg(self, opts, cb) {
     }
 }
 exports.renderSvg = renderSvg;
-//# sourceMappingURL=renderSvg.js.map

package/dist/shared/util.js

@@ -10,4 +10,3 @@ function hasPairedReads(features) {
     return false;
 }
 exports.hasPairedReads = hasPairedReads;
-//# sourceMappingURL=util.js.map

package/dist/util.js

@@ -129,4 +129,3 @@ function randomColor() {
     return `hsl(${Math.random() * 200}, 50%, 50%)`;
 }
 exports.randomColor = randomColor;
-//# sourceMappingURL=util.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -103,4 +103,3 @@ export default observer(function AlignmentFeatureDetails(props) {
         SA ? React.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (React.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
 });
-//# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -36,4 +36,3 @@ export default function AlignmentFlags(props) {
             return (React.createElement(FormControlLabel, { key: key, control: React.createElement(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
         }))));
 }
-//# sourceMappingURL=AlignmentsFeatureFlags.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js

@@ -28,4 +28,3 @@ export default function SupplementaryAlignments(props) {
                     }, href: "#" }, displayString)));
         }))));
 }
-//# sourceMappingURL=AlignmentsFeatureSuppAligns.js.map

package/esm/AlignmentsFeatureDetail/index.js

@@ -20,4 +20,3 @@ export default function register(pluginManager) {
     }));
 }
 export { configSchema };
-//# sourceMappingURL=index.js.map

package/esm/AlignmentsFeatureDetail/util.js

@@ -19,4 +19,3 @@ export async function navToLoc(locString, model) {
         session.notify(`${e}`);
     }
 }
-//# sourceMappingURL=util.js.map

package/esm/AlignmentsTrack/configSchemaF.js

@@ -13,4 +13,3 @@ export default function configSchemaFactory(pluginManager) {
         baseConfiguration: createBaseTrackConfig(pluginManager),
     });
 }
-//# sourceMappingURL=configSchemaF.js.map

package/esm/AlignmentsTrack/index.js

@@ -18,4 +18,3 @@ export default function register(pm) {
         return track;
     });
 }
-//# sourceMappingURL=index.js.map

package/esm/BamAdapter/BamAdapter.js

@@ -171,4 +171,3 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];
     }
 }
-//# sourceMappingURL=BamAdapter.js.map

package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -98,4 +98,3 @@ export default class BamSlightlyLazyFeature {
         return getClip(cigar, this.get('strand'));
     }
 }
-//# sourceMappingURL=BamSlightlyLazyFeature.js.map

package/esm/BamAdapter/configSchema.js

@@ -53,4 +53,3 @@ const configSchema = ConfigurationSchema('BamAdapter', {
     },
 }, { explicitlyTyped: true });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/BamAdapter/index.js

@@ -10,4 +10,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/CramAdapter/CramAdapter.js

@@ -222,4 +222,3 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }
 }
-//# sourceMappingURL=CramAdapter.js.map

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -135,4 +135,3 @@ export default class CramSlightlyLazyFeature {
         return readFeaturesToMismatches(readFeatures, start, qual);
     }
 }
-//# sourceMappingURL=CramSlightlyLazyFeature.js.map

package/esm/CramAdapter/CramTestAdapters.js

@@ -68,4 +68,3 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=CramTestAdapters.js.map

package/esm/CramAdapter/configSchema.js

@@ -45,4 +45,3 @@ const configSchema = ConfigurationSchema('CramAdapter', {
     },
 }, { explicitlyTyped: true });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/CramAdapter/index.js

@@ -11,4 +11,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/CramAdapter/util.js

@@ -233,4 +233,3 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
     }
     return cigar;
 }
-//# sourceMappingURL=util.js.map

package/esm/GuessAlignmentsTypes/index.js

@@ -51,4 +51,3 @@ export default (pluginManager) => {
         };
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -19,4 +19,3 @@ export default class HtsgetBamAdapter extends BamAdapter {
         return { bam };
     }
 }
-//# sourceMappingURL=HtsgetBamAdapter.js.map

package/esm/HtsgetBamAdapter/configSchema.js

@@ -31,4 +31,3 @@ const HtsgetBamAdapter = ConfigurationSchema('HtsgetBamAdapter', {
     },
 }, { explicitlyTyped: true });
 export default HtsgetBamAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/HtsgetBamAdapter/index.js

@@ -13,4 +13,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -2,6 +2,6 @@ import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;
-}): React.JSX.Element;
+}): React.JSX.Element | null;
 declare const _default: typeof AlignmentsDisplay;
 export default _default;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -11,9 +11,13 @@ const useStyles = makeStyles()({
     },
 });
 function AlignmentsDisplay({ model }) {
+    var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
-    const top = SNPCoverageDisplay.height;
+    if (!SNPCoverageDisplay) {
+        return null;
+    }
+    const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
     return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
         React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
             React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
@@ -28,4 +32,3 @@ function AlignmentsDisplay({ model }) {
             React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
 }
 export default observer(AlignmentsDisplay);
-//# sourceMappingURL=AlignmentsDisplay.js.map

package/esm/LinearAlignmentsDisplay/index.js

@@ -17,4 +17,3 @@ export default function (pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/esm/LinearAlignmentsDisplay/models/configSchema.js

@@ -31,4 +31,3 @@ export default function configModelFactory(pm) {
         explicitlyTyped: true,
     });
 }
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearAlignmentsDisplay/models/model.js

@@ -140,7 +140,8 @@ function stateModelFactory(pluginManager, configSchema) {
          * #method
          */
         searchFeatureByID(id) {
-            return self.PileupDisplay.searchFeatureByID(id);
+            var _a, _b;
+            return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
         },
         /**
          * #getter
@@ -270,6 +271,9 @@ function stateModelFactory(pluginManager, configSchema) {
              * #method
              */
             trackMenuItems() {
+                if (!self.PileupDisplay) {
+                    return [];
+                }
                 const extra = getLowerPanelDisplays(pluginManager).map(d => ({
                     type: 'radio',
                     label: d.displayName,
@@ -307,4 +311,3 @@ function stateModelFactory(pluginManager, configSchema) {
     });
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/LinearPileupDisplay/components/ColorByModifications.js

@@ -33,4 +33,3 @@ function ColorByTagDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(ColorByTagDlg);
-//# sourceMappingURL=ColorByModifications.js.map

package/esm/LinearPileupDisplay/components/ColorByTag.js

@@ -21,4 +21,3 @@ function ColorByTagDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
 }
 export default observer(ColorByTagDlg);
-//# sourceMappingURL=ColorByTag.js.map

package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -10,4 +10,3 @@ export default observer(function LinearPileupDisplayBlurb(props) {
             ? `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}`
             : null))) : null;
 });
-//# sourceMappingURL=LinearPileupDisplayBlurb.js.map

package/esm/LinearPileupDisplay/components/ModificationsTable.js

@@ -20,4 +20,3 @@ export default function ModificationTable({ modifications, }) {
                     background: value,
                 } })))))));
 }
-//# sourceMappingURL=ModificationsTable.js.map

package/esm/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -22,4 +22,3 @@ function SetFeatureHeightDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(SetFeatureHeightDlg);
-//# sourceMappingURL=SetFeatureHeight.js.map

package/esm/LinearPileupDisplay/components/SetMaxHeight.js

@@ -25,4 +25,3 @@ function SetMaxHeightDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(SetMaxHeightDlg);
-//# sourceMappingURL=SetMaxHeight.js.map

package/esm/LinearPileupDisplay/components/SortByTag.js

@@ -22,4 +22,3 @@ function SortByTagDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(SortByTagDlg);
-//# sourceMappingURL=SortByTag.js.map

package/esm/LinearPileupDisplay/configSchema.js

@@ -55,4 +55,3 @@ function configSchemaF(pluginManager) {
     });
 }
 export default configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearPileupDisplay/index.js

@@ -19,4 +19,3 @@ export default function register(pluginManager) {
 }
 export { default as linearPileupDisplayStateModelFactory } from './model';
 export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
-//# sourceMappingURL=index.js.map