@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -44,4 +44,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
     return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
         react_1.default.createElement(Cloud, { model: model })));
 });
-//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadCloudDisplay/configSchema.d.ts

@@ -33,14 +33,14 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     maxFeatureScreenDensity: {
         type: string;
         description: string;
-        defaultValue: number;
+        defaultValue: number; /**
+         * #slot
+         */
     };
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
-        description: string; /**
-         * #slot
-         */
+        description: string;
     };
     height: {
         type: string;

package/dist/LinearReadCloudDisplay/configSchema.js

@@ -48,4 +48,3 @@ function configSchemaF(pluginManager) {
     });
 }
 exports.default = configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -26,4 +26,3 @@ function drawFeats(self, ctx) {
     }
 }
 exports.drawFeats = drawFeats;
-//# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -66,4 +66,3 @@ function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     }
 }
 exports.drawLongReadChains = drawLongReadChains;
-//# sourceMappingURL=drawLongReadChains.js.map

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -97,4 +97,3 @@ function getPairedColor({ type, v0, v1, stats, }) {
     return undefined;
 }
 exports.getPairedColor = getPairedColor;
-//# sourceMappingURL=drawPairChains.js.map

package/dist/LinearReadCloudDisplay/index.js

@@ -24,4 +24,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -128,9 +128,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void; /**
-     * #property
-     */
+    setFeatureDensityStatsP(arg: any): void;
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {

package/dist/LinearReadCloudDisplay/model.js

@@ -224,4 +224,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LinearReadCloudDisplay/util.js

@@ -32,4 +32,3 @@ function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
     ctx.strokeRect(x, y, width, height);
 }
 exports.strokeRectCtx = strokeRectCtx;
-//# sourceMappingURL=util.js.map

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -58,4 +58,3 @@ const SNPCoverageTooltip = (0, mobx_react_1.observer)((props) => {
     return feat && feat.get('type') === 'skip' ? null : (react_1.default.createElement(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 exports.default = SNPCoverageTooltip;
-//# sourceMappingURL=Tooltip.js.map

package/dist/LinearSNPCoverageDisplay/index.js

@@ -22,4 +22,3 @@ function register(pluginManager) {
     });
 }
 exports.default = register;
-//# sourceMappingURL=index.js.map

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -62,6 +62,9 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         defaultValue: number;
     };
     fetchSizeLimit: {
+        /**
+         * #slot
+         */
         type: string;
         defaultValue: number;
         description: string;

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -73,4 +73,3 @@ function SNPCoverageConfigFactory(pluginManager) {
     });
 }
 exports.default = SNPCoverageConfigFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -21,7 +21,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
+             * #property
+             */
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
@@ -41,8 +43,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
+            /**
+             * #property
+             */
             model: any;
-        }) => any;
+        }) => any; /**
+         * #property
+         */
         renderProps: any;
     } & {
         doReload(): void;
@@ -51,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>; /**
-             * #getter
-             */
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -67,9 +72,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         maxFeatureScreenDensity: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: number;
         };
         fetchSizeLimit: {
@@ -96,11 +98,19 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
+    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
+    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+     * #property
+     */
     displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -190,7 +200,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any;
+    readonly adapterConfig: any; /**
+     * #getter
+     */
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
@@ -357,7 +369,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     reload(): Promise<void>;
 } & {
     readonly TooltipComponent: import("react").FC<{}>;
-    readonly rendererTypeName: string;
+    readonly rendererTypeName: string; /**
+     * #property
+     */
 } & {
     readonly ticks: {
         range: number[];
@@ -401,7 +415,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         subMenu: {
             label: string;
             type: string;
-            checked: boolean;
+            checked: boolean; /**
+             * #getter
+             */
             onClick: () => void;
         }[];
         type?: undefined;

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.d.ts

@@ -4,6 +4,6 @@ export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, SharedLinearPileupDisplayMixin, } from './LinearPileupDisplay';
 export { type LinearPileupDisplayModel } from './LinearPileupDisplay/model';
 export * as MismatchParser from './MismatchParser';

package/dist/index.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MismatchParser = exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
+exports.MismatchParser = exports.SharedLinearPileupDisplayMixin = exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const CramAdapter_1 = __importDefault(require("./CramAdapter"));
 const BamAdapter_1 = __importDefault(require("./BamAdapter"));
@@ -73,5 +73,5 @@ exports.default = AlignmentsPlugin;
 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; } });
+Object.defineProperty(exports, "SharedLinearPileupDisplayMixin", { enumerable: true, get: function () { return LinearPileupDisplay_2.SharedLinearPileupDisplayMixin; } });
 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.d.ts

@@ -1,3 +1,4 @@
+import { Instance } from 'mobx-state-tree';
 import { ChainStats } from './fetchChains';
 export declare const fillColor: {
     color_fwd_strand_not_proper: string;
@@ -53,3 +54,12 @@ export declare function getPairedInsertSizeAndOrientationColor(f1: {
 export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
 }): readonly [string, string];
+export interface ExtraColorBy {
+    custom?: Record<string, string>;
+}
+export declare const ColorByModel: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+    tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    extra: import("mobx-state-tree").IType<any, any, any>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+export type IColorByModel = Instance<typeof ColorByModel>;

package/dist/shared/color.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+exports.ColorByModel = exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../util");
 exports.fillColor = {
     color_fwd_strand_not_proper: '#ECC8C8',
@@ -74,4 +75,8 @@ function getPairedOrientationColor(f) {
     ];
 }
 exports.getPairedOrientationColor = getPairedOrientationColor;
-//# sourceMappingURL=color.js.map
+exports.ColorByModel = mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+    type: mobx_state_tree_1.types.string,
+    tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+    extra: mobx_state_tree_1.types.frozen(),
+}));

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