@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/dist/LinearSNPCoverageDisplay/model.js

@@ -27,103 +27,60 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const util_1 = require("@jbrowse/core/util");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-// locals
-const util_2 = require("../util");
+const util_1 = require("@jbrowse/core/util");
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const getUniqueModifications_1 = require("../shared/getUniqueModifications");
-// lazies
+const util_2 = require("../util");
 const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
-// using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-/**
- * #stateModel LinearSNPCoverageDisplay
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-        /**
-         * #property
-         */
         drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
         drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
         drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), {
-            flagInclude: 0,
-            flagExclude: 1540,
-        }),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
+        filterBySetting: mobx_state_tree_1.types.frozen(),
+        colorBySetting: mobx_state_tree_1.types.frozen(),
         jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         visibleModifications: mobx_1.observable.map({}),
-        /**
-         * #volatile
-         */
         modificationsReady: false,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setConfig(configuration) {
             self.configuration = configuration;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
-        /**
-         * #action
-         */
         setColorScheme(colorBy) {
-            self.colorBy = colorBy
+            self.colorBySetting = colorBy
                 ? {
                     ...colorBy,
                 }
                 : undefined;
         },
-        /**
-         * #action
-         */
         setJexlFilters(filters) {
             self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
         },
-        /**
-         * #action
-         */
         updateVisibleModifications(uniqueModifications) {
             for (const modification of uniqueModifications) {
                 if (!self.visibleModifications.has(modification.type)) {
@@ -138,9 +95,6 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { adapterProps: superAdapterProps } = self;
         return {
-            /**
-             * #getter
-             */
             get rendererConfig() {
                 const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
                 const { drawArcs, drawInterbaseCounts, drawIndicators } = self;
@@ -151,40 +105,24 @@ function stateModelFactory(pluginManager, configSchema) {
                     drawArcs: drawArcs !== null && drawArcs !== void 0 ? drawArcs : configBlob.drawArcs,
                 }, (0, mobx_state_tree_1.getEnv)(self));
             },
-            /**
-             * #getter
-             */
             get drawArcsSetting() {
                 var _a;
                 return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
             },
-            /**
-             * #getter
-             */
             get drawInterbaseCountsSetting() {
                 var _a;
                 return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
             },
-            /**
-             * #getter
-             */
             get drawIndicatorsSetting() {
                 var _a;
                 return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
             },
-            /**
-             * #getter
-             */
             get autorunReady() {
                 const view = (0, util_1.getContainingView)(self);
                 return (view.initialized &&
-                    self.featureDensityStatsReady &&
-                    !self.regionTooLarge &&
+                    self.statsReadyAndRegionNotTooLarge &&
                     !self.error);
             },
-            /**
-             * #method
-             */
             adapterProps() {
                 const superProps = superAdapterProps();
                 const { filters, filterBy } = self;
@@ -197,27 +135,15 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         setModificationsReady(flag) {
             self.modificationsReady = flag;
         },
-        /**
-         * #action
-         */
         toggleDrawIndicators() {
             self.drawIndicators = !self.drawIndicatorsSetting;
         },
-        /**
-         * #action
-         */
         toggleDrawInterbaseCounts() {
             self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
         },
-        /**
-         * #action
-         */
         toggleDrawArcs() {
             self.drawArcs = !self.drawArcsSetting;
         },
@@ -252,22 +178,13 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
         return {
-            /**
-             * #getter
-             */
             get renderReady() {
                 const superProps = superRenderProps();
                 return !superProps.notReady && self.modificationsReady;
             },
-            /**
-             * #getter
-             */
             get ready() {
                 return this.renderReady;
             },
-            /**
-             * #method
-             */
             renderProps() {
                 const { colorBy, visibleModifications } = self;
                 return {
@@ -277,15 +194,9 @@ function stateModelFactory(pluginManager, configSchema) {
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
                 };
             },
-            /**
-             * #getter
-             */
             get TooltipComponent() {
                 return Tooltip;
             },
-            /**
-             * #getter
-             */
             get adapterConfig() {
                 const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
                 return {
@@ -293,27 +204,15 @@ function stateModelFactory(pluginManager, configSchema) {
                     subadapter,
                 };
             },
-            /**
-             * #getter
-             */
             get rendererTypeName() {
                 return rendererTypes.get('snpcoverage');
             },
-            /**
-             * #getter
-             */
             get needsScalebar() {
                 return true;
             },
-            /**
-             * #method
-             */
             contextMenuItems() {
                 return [];
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -343,9 +242,6 @@ function stateModelFactory(pluginManager, configSchema) {
                     },
                 ];
             },
-            /**
-             * #getter
-             */
             get filters() {
                 return new serializableFilterChain_1.default({ filters: self.jexlFilters });
             },

package/dist/MismatchParser/cigarToMismatches.d.ts

@@ -1,3 +1,3 @@
-import { Mismatch } from '../shared/types';
+import type { Mismatch } from '../shared/types';
 import type { Buffer } from 'buffer';
 export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];

package/dist/MismatchParser/cigarToMismatches.js

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.cigarToMismatches = cigarToMismatches;
 function cigarToMismatches(ops, seq, ref, qual) {
-    let roffset = 0; // reference offset
-    let soffset = 0; // seq offset
+    let roffset = 0;
+    let soffset = 0;
     const mismatches = [];
     const hasRefAndSeq = ref && seq;
     for (let i = 0; i < ops.length; i += 2) {
@@ -12,10 +12,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
         if (op === 'M' || op === '=' || op === 'E') {
             if (hasRefAndSeq) {
                 for (let j = 0; j < len; j++) {
-                    if (
-                    // @ts-ignore in the full yarn build of the repo, this says that
-                    // object is possibly undefined for some reason, ignored
-                    seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()) {
+                    if (seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()) {
                         mismatches.push({
                             start: roffset + j,
                             type: 'mismatch',
@@ -60,7 +57,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
                 mismatches.push({
                     start: roffset + j,
                     type: 'mismatch',
-                    base: r[j],
+                    base: r[j] || 'X',
                     qual: q[j],
                     length: 1,
                 });

package/dist/MismatchParser/getNextRefPos.js

@@ -1,8 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getNextRefPos = getNextRefPos;
-// get relative reference sequence positions for positions given relative to
-// the read sequence
 function getNextRefPos(cigarOps, positions) {
     let readPos = 0;
     let refPos = 0;

package/dist/MismatchParser/index.d.ts

@@ -1,6 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Mismatch } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
 import type { Buffer } from 'buffer';
-import { Mismatch } from '../shared/types';
 export declare function parseCigar(cigar?: string): string[];
 export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];

package/dist/MismatchParser/index.js

@@ -11,8 +11,8 @@ exports.getLengthSansClipping = getLengthSansClipping;
 exports.getClip = getClip;
 exports.getTag = getTag;
 exports.featurizeSA = featurizeSA;
-const mdToMismatches_1 = require("./mdToMismatches");
 const cigarToMismatches_1 = require("./cigarToMismatches");
+const mdToMismatches_1 = require("./mdToMismatches");
 const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
@@ -22,11 +22,9 @@ function parseCigar(cigar = '') {
 function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];
     const ops = parseCigar(cigar);
-    // parse the CIGAR tag if it has one
     if (cigar) {
         mismatches = mismatches.concat((0, cigarToMismatches_1.cigarToMismatches)(ops, seq, ref, qual));
     }
-    // now let's look for CRAM or MD mismatches
     if (md && seq) {
         mismatches = mismatches.concat((0, mdToMismatches_1.mdToMismatches)(md, ops, mismatches, seq, qual));
     }
@@ -98,12 +96,6 @@ function getClip(cigar, strand) {
 function getTag(feature, tag) {
     return feature.get('tags')[tag];
 }
-// produces a list of "feature-like" object from parsing supplementary
-// alignments in the SA tag
-//
-// @param normalize - used specifically in the linear-read-vs-ref context, it
-// flips features around relative to the original feature. other contexts of
-// usage can keep this false
 function featurizeSA(SA, id, strand, readName, normalize) {
     return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
         const ret = aln.split(',');

package/dist/MismatchParser/mdToMismatches.d.ts

@@ -1,3 +1,3 @@
-import { Mismatch } from '../shared/types';
-import { Buffer } from 'buffer';
+import type { Mismatch } from '../shared/types';
+import type { Buffer } from 'buffer';
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer | number[] | null): Mismatch[];

package/dist/MismatchParser/mdToMismatches.js

@@ -10,11 +10,8 @@ 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,
@@ -43,7 +40,6 @@ 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;
@@ -54,8 +50,6 @@ 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/dist/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/dist/ModificationParser/index.js

@@ -5,17 +5,9 @@ exports.getModPositions = getModPositions;
 exports.getModTypes = getModTypes;
 exports.getMethBins = getMethBins;
 const util_1 = require("@jbrowse/core/util");
-const util_2 = require("../util");
 const MismatchParser_1 = require("../MismatchParser");
+const util_2 = require("../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
 function getModProbabilities(feature) {
     var _a;
     const m = (0, util_2.getTagAlt)(feature, 'ML', 'Ml') || [];
@@ -29,15 +21,11 @@ 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');
@@ -48,7 +36,6 @@ 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 = [];
@@ -63,8 +50,6 @@ 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);
                     }
                 }
@@ -93,8 +78,6 @@ 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/dist/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/dist/PileupRPC/base.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
 const util_1 = require("@jbrowse/core/util");
-// specialized get features to return limited data about alignments
 class PileupBaseRPC extends RpcMethodType_1.default {
     async serializeArguments(args, rpcDriver) {
         var _a;

package/dist/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/dist/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/dist/PileupRPC/methods/GetGlobalValueForTag.js

@@ -4,9 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
-// locals
+const operators_1 = require("rxjs/operators");
 const base_1 = __importDefault(require("../base"));
 class PileupGetGlobalValueForTag extends base_1.default {
     constructor() {

package/dist/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/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -5,13 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const util_1 = require("@jbrowse/core/util");
-const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
-// locals
-const util_2 = require("../util");
-const base_1 = __importDefault(require("../base"));
+const operators_1 = require("rxjs/operators");
 const MismatchParser_1 = require("../../MismatchParser");
-// specialized get features to return limited data about alignments
+const base_1 = __importDefault(require("../base"));
+const util_2 = require("../util");
 class PileupGetReducedFeatures extends base_1.default {
     constructor() {
         super(...arguments);

package/dist/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/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
+const operators_1 = require("rxjs/operators");
 const ModificationParser_1 = require("../../ModificationParser");
 const util_1 = require("../../util");
 const base_1 = __importDefault(require("../base"));

package/dist/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/dist/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/dist/PileupRenderer/PileupLayoutSession.js

@@ -4,12 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupLayoutSession = void 0;
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
 const configuration_1 = require("@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
+const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 class PileupLayoutSession extends BoxRendererType_1.LayoutSession {
     constructor(args) {
         super(args);