@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/MismatchParser/mdToMismatches.js

@@ -7,11 +7,8 @@ export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
     let lastSkipPos = 0;
     const mismatchRecords = [];
     const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
-    // convert a position on the reference sequence to a position on the template
-    // sequence, taking into account hard and soft clipping of reads
     function nextRecord() {
         mismatchRecords.push(curr);
-        // get a new mismatch record ready
         curr = {
             start: curr.start + curr.length,
             length: 0,
@@ -40,7 +37,6 @@ export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
         lastRefOffset = refOffset;
         return templateOffset - (refOffset - refCoord);
     }
-    // now actually parse the MD string
     const md = mdstring.match(mdRegex) || [];
     for (const token of md) {
         const num = +token;
@@ -51,8 +47,6 @@ export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
             curr.start += token.length - 1;
         }
         else {
-            // mismatch
-            // eslint-disable-next-line @typescript-eslint/prefer-for-of
             for (let j = 0; j < token.length; j += 1) {
                 curr.length = 1;
                 while (lastSkipPos < skips.length) {

package/esm/ModificationParser/index.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export declare function getModProbabilities(feature: Feature): number[] | undefined;
 export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
     type: string;

package/esm/ModificationParser/index.js

@@ -1,15 +1,7 @@
 import { revcom } from '@jbrowse/core/util';
-import { getTagAlt } from '../util';
 import { getNextRefPos } from '../MismatchParser';
+import { getTagAlt } from '../util';
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
-// ML stores probabilities as array of numerics and MP is scaled phred scores
-// https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596
-//
-// if we have ML or Ml, it is an 8bit probability, divide by 255
-//
-// if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but has
-// very high likelihood basecalls at that point, we really only care about low
-// qual calls <20 approx
 export function getModProbabilities(feature) {
     var _a;
     const m = getTagAlt(feature, 'ML', 'Ml') || [];
@@ -23,15 +15,11 @@ export function getModPositions(mm, fseq, fstrand) {
     const result = [];
     for (const mod of mods) {
         const [basemod, ...skips] = mod.split(',');
-        // regexes based on parse_mm.pl from hts-specs
-        // https://github.com/samtools/hts-specs/blob/master/test/SAMtags/parse_mm.pl
         const matches = modificationRegex.exec(basemod);
         if (!matches) {
             throw new Error('bad format for MM tag');
         }
         const [, base, strand, typestr] = matches;
-        // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so split,
-        // and they can also be chemical codes (ChEBI) e.g. C+16061
         const types = typestr.split(/(\d+|.)/).filter(f => !!f);
         if (strand === '-') {
             console.warn('unsupported negative strand modifications');
@@ -42,7 +30,6 @@ export function getModPositions(mm, fseq, fstrand) {
                 strand: strand,
             });
         }
-        // this logic based on parse_mm.pl from hts-specs
         for (const type of types) {
             let i = 0;
             const positions = [];
@@ -57,8 +44,6 @@ export function getModPositions(mm, fseq, fstrand) {
                 if (fstrand === -1) {
                     const pos = seq.length - i;
                     if (pos >= 0) {
-                        // avoid negative-number-positions in array, seen in #4629 cause
-                        // unknown, could warrant some further investigation
                         positions.unshift(pos);
                     }
                 }
@@ -87,8 +72,6 @@ export function getModTypes(mm) {
             throw new Error('bad format for MM tag');
         }
         const [, base, strand, typestr] = matches;
-        // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
-        // split, and they can also be chemical codes (ChEBI) e.g. C+16061
         return typestr
             .split(/(\d+|.)/)
             .filter(f => !!f)

package/esm/PileupRPC/base.d.ts

@@ -1,8 +1,8 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
 export default abstract class PileupBaseRPC extends RpcMethodType {
     serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
+        stopToken?: string;
         statusCallback?: (arg: string) => void;
     }, rpcDriver: string): Promise<Record<string, unknown>>;
 }

package/esm/PileupRPC/base.js

@@ -1,6 +1,5 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
 import { renameRegionsIfNeeded } from '@jbrowse/core/util';
-// specialized get features to return limited data about alignments
 export default class PileupBaseRPC extends RpcMethodType {
     async serializeArguments(args, rpcDriver) {
         var _a;

package/esm/PileupRPC/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function PileupRPCMethodsF(pm: PluginManager): void;

package/esm/PileupRPC/index.js

@@ -1,4 +1,4 @@
-import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, PileupGetReducedFeatures, } from './rpcMethods';
+import { PileupGetGlobalValueForTag, PileupGetReducedFeatures, PileupGetVisibleModifications, } from './rpcMethods';
 export default function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));

package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts

@@ -1,11 +1,10 @@
-import { Region } from '@jbrowse/core/util';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 import PileupBaseRPC from '../base';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
     name: string;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;

package/esm/PileupRPC/methods/GetGlobalValueForTag.js

@@ -1,7 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
-// locals
+import { toArray } from 'rxjs/operators';
 import PileupBaseRPC from '../base';
 export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
     constructor() {

package/esm/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,11 +1,10 @@
-import { Region } from '@jbrowse/core/util';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 import PileupBaseRPC from '../base';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupGetReducedFeatures extends PileupBaseRPC {
     name: string;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -1,12 +1,10 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { dedupe, groupBy } from '@jbrowse/core/util';
-import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
-// locals
-import { filterForPairs, getInsertSizeStats } from '../util';
-import PileupBaseRPC from '../base';
+import { toArray } from 'rxjs/operators';
 import { getClip } from '../../MismatchParser';
-// specialized get features to return limited data about alignments
+import PileupBaseRPC from '../base';
+import { filterForPairs, getInsertSizeStats } from '../util';
 export default class PileupGetReducedFeatures extends PileupBaseRPC {
     constructor() {
         super(...arguments);

package/esm/PileupRPC/methods/GetVisibleModifications.d.ts

@@ -1,12 +1,11 @@
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { Region } from '@jbrowse/core/util';
-import { ModificationType } from '../../shared/types';
 import PileupBaseRPC from '../base';
+import type { ModificationType } from '../../shared/types';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
     name: string;
     execute(args: {
         adapterConfig: Record<string, unknown>;
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -1,6 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import { getModTypes } from '../../ModificationParser';
 import { getTagAlt } from '../../util';
 import PileupBaseRPC from '../base';

package/esm/PileupRPC/util.d.ts

@@ -1,4 +1,4 @@
-import { ReducedFeature } from '../shared/fetchChains';
+import type { ReducedFeature } from '../shared/fetchChains';
 export declare function getInsertSizeStats(features: ReducedFeature[]): {
     upper: number;
     lower: number;

package/esm/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,9 +1,9 @@
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
-import { FilterBy, SortedBy } from '../shared/types';
+import type { FilterBy, SortedBy } from '../shared/types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import type GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import type MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
 export interface PileupLayoutSessionProps {
     config: AnyConfigurationModel;
     bpPerPx: number;

package/esm/PileupRenderer/PileupLayoutSession.js

@@ -1,9 +1,6 @@
-import deepEqual from 'fast-deep-equal';
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { readConfObject } from '@jbrowse/core/configuration';
-// The pileup layout session adds
-// - sorting and revealing soft clip changes the layout of pileup renderer
-// - extra conditions to see if cached layout is valid
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import deepEqual from 'fast-deep-equal';
 export class PileupLayoutSession extends LayoutSession {
     constructor(args) {
         super(args);

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -1,29 +1,16 @@
-import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Feature, Region } from '@jbrowse/core/util';
-import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
-import { ColorBy, ModificationTypeWithColor, SortedBy } from '../shared/types';
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    colorBy?: ColorBy;
-    colorTagMap?: Record<string, string>;
-    visibleModifications?: Record<string, ModificationTypeWithColor>;
-    sortedBy?: SortedBy;
-    showSoftClip: boolean;
-    highResolutionScaling: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    layout: BaseLayout<Feature>;
-    regionSequence?: string;
-}
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { PileupLayoutSession } from './PileupLayoutSession';
+import type { PileupLayoutSessionProps } from './PileupLayoutSession';
+import type { RenderArgsDeserialized } from './types';
+import type { Region } from '@jbrowse/core/util';
 export default class PileupRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    fetchSequence(renderProps: RenderArgsDeserialized, region: Region): Promise<any>;
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
-        reversed?: boolean | undefined;
         refName: string;
+        reversed?: boolean | undefined;
         assemblyName: string;
     };
     render(renderProps: RenderArgsDeserialized): Promise<{
@@ -32,8 +19,9 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
+        containsNoTransferables: boolean;
         canvasRecordedData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
@@ -41,7 +29,8 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
-        reactElement: React.JSX.Element;
+        containsNoTransferables: boolean;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         html?: string;
     } | {
         features: Map<any, any>;
@@ -49,10 +38,11 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
+        containsNoTransferables: boolean;
         imageData: any;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
-export type { RenderArgs, RenderResults, RenderArgsSerialized, ResultsSerialized, ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/esm/PileupRenderer/PileupRenderer.js

@@ -1,9 +1,8 @@
-import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { notEmpty, renderToAbstractCanvas, } from '@jbrowse/core/util';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { PileupLayoutSession, } from './PileupLayoutSession';
-// locals
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { renderToAbstractCanvas } from '@jbrowse/core/util';
+import { PileupLayoutSession } from './PileupLayoutSession';
 import { fetchSequence } from '../util';
 import { layoutFeats } from './layoutFeatures';
 export default class PileupRenderer extends BoxRendererType {
@@ -11,14 +10,13 @@ export default class PileupRenderer extends BoxRendererType {
         super(...arguments);
         this.supportsSVG = true;
     }
-    async fetchSequence(renderProps) {
-        const { sessionId, regions, adapterConfig } = renderProps;
+    async fetchSequence(renderProps, region) {
+        const { sessionId, adapterConfig } = renderProps;
         const { sequenceAdapter } = adapterConfig;
         if (!sequenceAdapter) {
             return undefined;
         }
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, sequenceAdapter);
-        const region = regions[0];
         return fetchSequence({
             ...region,
             start: Math.max(0, region.start - 1),
@@ -31,7 +29,6 @@ export default class PileupRenderer extends BoxRendererType {
         const maxClippingSize = readConfObject(config, 'maxClippingSize');
         const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...region,
             start: Math.floor(Math.max(start - bpExpansion, 0)),
             end: Math.ceil(end + bpExpansion),
@@ -40,25 +37,22 @@ export default class PileupRenderer extends BoxRendererType {
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
-        const { regions, bpPerPx } = renderProps;
+        const { colorBy, regions, bpPerPx } = renderProps;
         const region = regions[0];
-        const layoutRecords = layoutFeats({
+        const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
+            ? await this.fetchSequence(renderProps, region)
+            : undefined;
+        const { layoutRecords, height } = layoutFeats({
             ...renderProps,
             features,
             layout,
         });
-        // only need reference sequence if there are features and only for some
-        // cases
-        const regionSequence = features.size
-            ? await this.fetchSequence(renderProps)
-            : undefined;
         const width = (region.end - region.start) / bpPerPx;
-        const height = Math.max(layout.getTotalHeight(), 1);
         const { makeImageData } = await import('./makeImageData');
         const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
             makeImageData({
                 ctx,
-                layoutRecords: layoutRecords.filter(notEmpty),
+                layoutRecords,
                 canvasWidth: width,
                 renderArgs: {
                     ...renderProps,
@@ -85,6 +79,7 @@ export default class PileupRenderer extends BoxRendererType {
             height,
             width,
             maxHeightReached: layout.maxHeightReached,
+            containsNoTransferables: true,
         };
     }
     createSession(args) {

package/esm/PileupRenderer/colorBy.d.ts

@@ -1,5 +1,5 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function colorByInsertSize(feature: Feature): string;
 export declare function colorByMappingQuality(feature: Feature): string;
 export declare function colorByStrand(feature: Feature): "#EC8B8B" | "#8F8FD8";

package/esm/PileupRenderer/colorBy.js

@@ -1,4 +1,4 @@
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { fillColor } from '../shared/color';
 import { orientationTypes } from '../util';
 export function colorByInsertSize(feature) {
@@ -30,27 +30,21 @@ export function colorByOrientation(feature, config) {
 function getStranded(feature) {
     const flags = feature.get('flags');
     const strand = feature.get('strand');
-    // is paired
     if (flags & 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';
         }
-        // mate missing, separate color
         if (flags & 8) {
             return strand * flipper === 1
                 ? 'color_rev_missing_mate'
                 : 'color_fwd_missing_mate';
         }
-        // same chrom without proper pairing gets separate color
         if (feature.get('refName') === feature.get('next_ref')) {
             return strand * flipper === 1
                 ? 'color_rev_strand_not_proper'
                 : 'color_fwd_strand_not_proper';
         }
-        // abberant chrom
         return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
     }
     return 'color_unknown';

package/esm/PileupRenderer/components/PileupRendering.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
+import type { Region } from '@jbrowse/core/util/types';
 import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
 declare const PileupRendering: (props: {
     blockKey: string;
@@ -23,5 +22,5 @@ declare const PileupRendering: (props: {
         };
     };
     onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default PileupRendering;

package/esm/PileupRenderer/components/PileupRendering.js

@@ -1,4 +1,5 @@
-import React, { useRef, useState, useEffect } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useRef, useState } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { bpSpanPx } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
@@ -81,9 +82,7 @@ const PileupRendering = observer(function (props) {
         onMouseMove === null || onMouseMove === void 0 ? void 0 : onMouseMove(event, displayModel === null || displayModel === void 0 ? void 0 : displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY));
     }
     function callMouseHandler(handlerName, event) {
-        // @ts-expect-error
         const featureHandler = props[`onFeature${handlerName}`];
-        // @ts-expect-error
         const canvasHandler = props[`on${handlerName}`];
         if (featureHandler && featureIdUnderMouse) {
             featureHandler(event, featureIdUnderMouse);
@@ -93,8 +92,7 @@ const PileupRendering = observer(function (props) {
         }
     }
     const canvasWidth = Math.ceil(width);
-    // need to call this in render so we get the right observer behavior
-    return (React.createElement("div", { ref: ref, "data-testid": [
+    return (_jsxs("div", { ref: ref, "data-testid": [
             'pileup-overlay',
             sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type,
             colorBy === null || colorBy === void 0 ? void 0 : colorBy.type,
@@ -120,20 +118,17 @@ const PileupRendering = observer(function (props) {
             onClick(event);
         }, onContextMenu: event => {
             onContextMenu(event);
-        }, onFocus: () => { }, onBlur: () => { } },
-        React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }),
-        firstRender && highlight ? (React.createElement("div", { style: {
-                position: 'absolute',
-                backgroundColor: '#0003',
-                pointerEvents: 'none',
-                ...highlight,
-            } })) : null,
-        firstRender && selected ? (React.createElement("div", { style: {
-                position: 'absolute',
-                border: '2px solid #00b8ff',
-                boxSizing: 'content-box',
-                pointerEvents: 'none',
-                ...selected,
-            } })) : null));
+        }, onFocus: () => { }, onBlur: () => { }, children: [_jsx(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }), firstRender && highlight ? (_jsx("div", { style: {
+                    position: 'absolute',
+                    backgroundColor: '#0003',
+                    pointerEvents: 'none',
+                    ...highlight,
+                } })) : null, firstRender && selected ? (_jsx("div", { style: {
+                    position: 'absolute',
+                    border: '2px solid #00b8ff',
+                    boxSizing: 'content-box',
+                    pointerEvents: 'none',
+                    ...selected,
+                } })) : null] }));
 });
 export default PileupRendering;

package/esm/PileupRenderer/configSchema.d.ts

@@ -1,84 +1,58 @@
 declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * default magenta here is used to detect the user has not customized this
-     */
     color: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     orientationType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     displayMode: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     minSubfeatureWidth: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
+    hideSmallIndels: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
     maxHeight: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     maxClippingSize: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     height: {
         type: string;
         description: string;
         defaultValue: number;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     noSpacing: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     largeInsertionIndicatorScale: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     mismatchAlpha: {
         type: string;
         defaultValue: boolean;