@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/esm/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/esm/LinearReadCloudDisplay/configSchema.js

@@ -46,4 +46,3 @@ function configSchemaF(pluginManager) {
     });
 }
 export default configSchemaF;
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -22,4 +22,3 @@ export function drawFeats(self, ctx) {
         drawLongReadChains({ self, view, asm, ctx, chainData });
     }
 }
-//# sourceMappingURL=drawFeats.js.map

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -62,4 +62,3 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
         }
     }
 }
-//# sourceMappingURL=drawLongReadChains.js.map

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -92,4 +92,3 @@ export function getPairedColor({ type, v0, v1, stats, }) {
     }
     return undefined;
 }
-//# sourceMappingURL=drawPairChains.js.map

package/esm/LinearReadCloudDisplay/index.js

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

package/esm/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/esm/LinearReadCloudDisplay/model.js

@@ -196,4 +196,3 @@ function stateModelFactory(configSchema) {
     }));
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/LinearReadCloudDisplay/util.js

@@ -27,4 +27,3 @@ export function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
     }
     ctx.strokeRect(x, y, width, height);
 }
-//# sourceMappingURL=util.js.map

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -53,4 +53,3 @@ const SNPCoverageTooltip = observer((props) => {
     return feat && feat.get('type') === 'skip' ? null : (React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 export default SNPCoverageTooltip;
-//# sourceMappingURL=Tooltip.js.map

package/esm/LinearSNPCoverageDisplay/index.js

@@ -16,4 +16,3 @@ export default function register(pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/esm/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/esm/LinearSNPCoverageDisplay/models/configSchema.js

@@ -70,4 +70,3 @@ export default function SNPCoverageConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-//# sourceMappingURL=configSchema.js.map

package/esm/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/esm/LinearSNPCoverageDisplay/models/model.js

@@ -268,4 +268,3 @@ function stateModelFactory(pluginManager, configSchema) {
     });
 }
 export default stateModelFactory;
-//# sourceMappingURL=model.js.map

package/esm/MismatchParser/index.js

@@ -428,4 +428,3 @@ export function featurizeSA(SA, id, strand, readName, normalize) {
         };
     })) || []);
 }
-//# sourceMappingURL=index.js.map

package/esm/PileupRPC/base.js

@@ -13,4 +13,3 @@ export default class PileupBaseRPC extends RpcMethodType {
         return super.serializeArguments(renamedArgs, rpcDriver);
     }
 }
-//# sourceMappingURL=base.js.map

package/esm/PileupRPC/index.js

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

package/esm/PileupRPC/methods/GetGlobalValueForTag.js

@@ -22,4 +22,3 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
         ];
     }
 }
-//# sourceMappingURL=GetGlobalValueForTag.js.map

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -43,4 +43,3 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
         };
     }
 }
-//# sourceMappingURL=GetReducedFeatures.js.map

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -21,4 +21,3 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
         return [...uniqueValues];
     }
 }
-//# sourceMappingURL=GetVisibleModifications.js.map

package/esm/PileupRPC/rpcMethods.js

@@ -1,4 +1,3 @@
 export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
 export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
 export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';
-//# sourceMappingURL=rpcMethods.js.map

package/esm/PileupRPC/util.js

@@ -12,4 +12,3 @@ export function getInsertSizeStats(features) {
 export function filterForPairs(features) {
     return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
 }
-//# sourceMappingURL=util.js.map

package/esm/PileupRenderer/PileupLayoutSession.js

@@ -29,4 +29,3 @@ export class PileupLayoutSession extends LayoutSession {
         return this.cachedLayout.layout;
     }
 }
-//# sourceMappingURL=PileupLayoutSession.js.map

package/esm/PileupRenderer/PileupRenderer.js

@@ -88,4 +88,3 @@ export default class PileupRenderer extends BoxRendererType {
         return new PileupLayoutSession(args);
     }
 }
-//# sourceMappingURL=PileupRenderer.js.map

package/esm/PileupRenderer/colorBy.js

@@ -32,30 +32,31 @@ 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';
 }
 export function colorByStrandedRnaSeq(feature) {
     return fillColor[getStranded(feature)];
 }
-//# sourceMappingURL=colorBy.js.map

package/esm/PileupRenderer/components/PileupRendering.js

@@ -134,4 +134,3 @@ function PileupRendering(props) {
         React.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: () => { } })));
 }
 export default observer(PileupRendering);
-//# sourceMappingURL=PileupRendering.js.map

package/esm/PileupRenderer/configSchema.js

@@ -96,4 +96,3 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
     },
 }, { explicitlyTyped: true });
 export default PileupRenderer;
-//# sourceMappingURL=configSchema.js.map

package/esm/PileupRenderer/getAlignmentShapeColor.js

@@ -53,4 +53,3 @@ export function getAlignmentShapeColor({ colorType, tag, feature, config, defaul
                 : readConfObject(config, 'color', { feature });
     }
 }
-//# sourceMappingURL=getAlignmentShapeColor.js.map

package/esm/PileupRenderer/index.js

@@ -12,4 +12,3 @@ export default function register(pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/esm/PileupRenderer/layoutFeature.js

@@ -34,4 +34,3 @@ export function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip,
         heightPx,
     };
 }
-//# sourceMappingURL=layoutFeature.js.map

package/esm/PileupRenderer/layoutFeatures.js

@@ -28,4 +28,3 @@ export function layoutFeats(props) {
         displayMode,
     }), featureMap.size);
 }
-//# sourceMappingURL=layoutFeatures.js.map

package/esm/PileupRenderer/makeImageData.js

@@ -57,4 +57,3 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
         }
     }
 }
-//# sourceMappingURL=makeImageData.js.map

package/esm/PileupRenderer/renderAlignment.js

@@ -65,4 +65,3 @@ export function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastF
             break;
     }
 }
-//# sourceMappingURL=renderAlignment.js.map

package/esm/PileupRenderer/renderAlignmentShape.js

@@ -8,7 +8,7 @@ export function renderAlignmentShape({ ctx, feat, renderArgs, }) {
     const [leftPx, rightPx] = 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);
@@ -34,4 +34,3 @@ export function renderAlignmentShape({ ctx, feat, renderArgs, }) {
         ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
     }
 }
-//# sourceMappingURL=renderAlignmentShape.js.map

package/esm/PileupRenderer/renderMethylation.js

@@ -56,4 +56,3 @@ export function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canv
         }
     }
 }
-//# sourceMappingURL=renderMethylation.js.map

package/esm/PileupRenderer/renderMismatches.js

@@ -128,4 +128,3 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
         }
     }
 }
-//# sourceMappingURL=renderMismatches.js.map

package/esm/PileupRenderer/renderModifications.js

@@ -47,4 +47,3 @@ export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, ca
         }
     }
 }
-//# sourceMappingURL=renderModifications.js.map

package/esm/PileupRenderer/renderPerBaseLettering.js

@@ -40,4 +40,3 @@ export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBas
         }
     }
 }
-//# sourceMappingURL=renderPerBaseLettering.js.map

package/esm/PileupRenderer/renderPerBaseQuality.js

@@ -32,4 +32,3 @@ export function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth,
         }
     }
 }
-//# sourceMappingURL=renderPerBaseQuality.js.map

package/esm/PileupRenderer/renderSoftClipping.js

@@ -41,4 +41,3 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
         }
     });
 }
-//# sourceMappingURL=renderSoftClipping.js.map

package/esm/PileupRenderer/sortUtil.js

@@ -77,4 +77,3 @@ export const sortFeature = (features, sortedBy) => {
         feature,
     ]));
 };
-//# sourceMappingURL=sortUtil.js.map

package/esm/PileupRenderer/util.js

@@ -39,4 +39,3 @@ export function getCharWidthHeight() {
     const charHeight = measureText('M') - 2;
     return { charWidth, charHeight };
 }
-//# sourceMappingURL=util.js.map

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -75,4 +75,3 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=SNPCoverageAdapter.js.map

package/esm/SNPCoverageAdapter/configSchema.js

@@ -14,4 +14,3 @@ const configSchema = ConfigurationSchema('SNPCoverageAdapter', {
     },
 }, { explicitlyTyped: true });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -206,4 +206,3 @@ export default async function generateCoverageBins(features, region, opts, fetch
     }
     return { bins, skipmap };
 }
-//# sourceMappingURL=generateCoverageBins.js.map

package/esm/SNPCoverageAdapter/index.js

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

package/esm/SNPCoverageAdapter/util.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=util.js.map

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -184,4 +184,3 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         }
     }
 }
-//# sourceMappingURL=SNPCoverageRenderer.js.map

package/esm/SNPCoverageRenderer/configSchema.js

@@ -51,4 +51,3 @@ const SNPCoverageRenderer = ConfigurationSchema('SNPCoverageRenderer', {
     },
 }, { explicitlyTyped: true });
 export default SNPCoverageRenderer;
-//# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageRenderer/index.js

@@ -9,4 +9,3 @@ export default function register(pluginManager) {
         pluginManager,
     }));
 }
-//# sourceMappingURL=index.js.map

package/esm/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/esm/index.js

@@ -40,6 +40,5 @@ export default class AlignmentsPlugin extends Plugin {
         ].map(f => f(pluginManager));
     }
 }
-export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, SharedLinearPileupDisplayMixin, } from './LinearPileupDisplay';
 export * as MismatchParser from './MismatchParser';
-//# sourceMappingURL=index.js.map

package/esm/shared/BaseDisplayComponent.js

@@ -41,4 +41,3 @@ const LoadingBar = observer(function ({ model, }) {
     return (React.createElement("div", { className: classes.loading },
         React.createElement(LoadingEllipses, { message: message })));
 });
-//# sourceMappingURL=BaseDisplayComponent.js.map

package/esm/shared/FilterByTag.js

@@ -99,4 +99,3 @@ function FilterByTagDlg(props) {
                 React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(FilterByTagDlg);
-//# sourceMappingURL=FilterByTag.js.map

package/esm/shared/afterAttach.js

@@ -37,4 +37,3 @@ export function doAfterAttach(self, cb) {
         draw(view);
     }, { delay: 1000 });
 }
-//# sourceMappingURL=afterAttach.js.map

package/esm/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/esm/shared/color.js

@@ -1,3 +1,4 @@
+import { types } from 'mobx-state-tree';
 import { orientationTypes, pairMap } from '../util';
 export const fillColor = {
     color_fwd_strand_not_proper: '#ECC8C8',
@@ -68,4 +69,8 @@ export function getPairedOrientationColor(f) {
         strokeColor[type2] || strokeColor.color_unknown,
     ];
 }
-//# sourceMappingURL=color.js.map
+export const ColorByModel = types.maybe(types.model({
+    type: types.string,
+    tag: types.maybe(types.string),
+    extra: types.frozen(),
+}));

package/esm/shared/fetchChains.js

@@ -17,4 +17,3 @@ export async function fetchChains(self) {
     self.setChainData(ret);
     self.setLoading(false);
 }
-//# sourceMappingURL=fetchChains.js.map

package/esm/shared/index.js

@@ -35,4 +35,3 @@ export const FilterModel = types.model({
         value: types.string,
     })),
 });
-//# sourceMappingURL=index.js.map

package/esm/shared/renderSvg.js

@@ -36,4 +36,3 @@ export async function renderSvg(self, opts, cb) {
                 dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
     }
 }
-//# sourceMappingURL=renderSvg.js.map

package/esm/shared/util.js

@@ -6,4 +6,3 @@ export function hasPairedReads(features) {
     }
     return false;
 }
-//# sourceMappingURL=util.js.map

package/esm/util.js

@@ -119,4 +119,3 @@ export function createAutorun(self, cb, opts) {
 export function randomColor() {
     return `hsl(${Math.random() * 200}, 50%, 50%)`;
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,8 +20,7 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "esm",
-    "src"
+    "esm"
   ],
   "scripts": {
     "build": "npm-run-all build:*",
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -65,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +0,0 @@
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