@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/esm/MismatchParser/index.js

@@ -1,11 +1,11 @@
-import { cigarToMismatches } from './cigarToMismatches';
-import { mdToMismatches } from './mdToMismatches';
+import { cigarToMismatches } from "./cigarToMismatches.js";
+import { cigarToMismatches2 } from "./cigarToMismatches2.js";
+import { mdToMismatches } from "./mdToMismatches.js";
+import { mdToMismatches2 } from "./mdToMismatches2.js";
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
 export function parseCigar(s = '') {
     let currLen = '';
-    let len;
-    let op;
     const ret = [];
     for (let i = 0, l = s.length; i < l; i++) {
         const c = s[i];
@@ -13,14 +13,39 @@ export function parseCigar(s = '') {
             currLen = currLen + c;
         }
         else {
-            len = currLen;
-            op = c;
+            ret.push(currLen, c);
             currLen = '';
-            ret.push(len, op);
         }
     }
     return ret;
 }
+const CIGAR_CODE_TO_INDEX = {
+    77: 0,
+    73: 1,
+    68: 2,
+    78: 3,
+    83: 4,
+    72: 5,
+    80: 6,
+    61: 7,
+    88: 8,
+};
+export function parseCigar2(s = '') {
+    let currLen = 0;
+    const ret = [];
+    for (let i = 0, l = s.length; i < l; i++) {
+        const code = s.charCodeAt(i);
+        if (code >= 48 && code <= 57) {
+            currLen = currLen * 10 + (code - 48);
+        }
+        else {
+            const opIndex = CIGAR_CODE_TO_INDEX[code];
+            ret.push((currLen << 4) | opIndex);
+            currLen = 0;
+        }
+    }
+    return new Uint32Array(ret);
+}
 export function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];
     const ops = parseCigar(cigar);
@@ -32,6 +57,16 @@ export function getMismatches(cigar, md, seq, ref, qual) {
     }
     return mismatches;
 }
+export function getMismatches2(cigar, md, seq, ref, qual) {
+    let mismatches = [];
+    if (cigar && cigar.length > 0) {
+        mismatches = mismatches.concat(cigarToMismatches2(cigar, seq, ref, qual));
+    }
+    if (md && seq && cigar) {
+        mismatches = mismatches.concat(mdToMismatches2(md, cigar, mismatches, seq, qual));
+    }
+    return mismatches;
+}
 export function getOrientedCigar(flip, cigar) {
     if (flip) {
         const ret = [];
@@ -99,7 +134,9 @@ export function getTag(feature, tag) {
     return feature.get('tags')[tag];
 }
 export function featurizeSA(SA, id, strand, readName, normalize) {
-    return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
+    return (SA?.split(';')
+        .filter(aln => !!aln)
+        .map((aln, index) => {
         const ret = aln.split(',');
         const saRef = ret[0];
         const saStart = ret[1];
@@ -116,7 +153,7 @@ export function featurizeSA(SA, id, strand, readName, normalize) {
             start: saRealStart,
             end: saRealStart + saLengthOnRef,
             seqLength: saLength,
-            clipPos: saClipPos,
+            clipLengthAtStartOfRead: saClipPos,
             CIGAR: saCigar,
             strand: (normalize ? strand : 1) * saStrandNormalized,
             uniqueId: `${id}_SA${index}`,
@@ -126,6 +163,7 @@ export function featurizeSA(SA, id, strand, readName, normalize) {
                 refName: readName,
             },
         };
-    })) || []);
+    }) || []);
 }
-export { getNextRefPos } from './getNextRefPos';
+export { getNextRefPos } from "./getNextRefPos.js";
+export { cigarToMismatches2 } from "./cigarToMismatches2.js";

package/esm/MismatchParser/mdToMismatches.d.ts

@@ -1,2 +1,2 @@
-import type { Mismatch } from '../shared/types';
+import type { Mismatch } from '../shared/types.ts';
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Uint8Array): Mismatch[];

package/esm/MismatchParser/mdToMismatches.js

@@ -1,70 +1,104 @@
-const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
-    let curr = { start: 0, base: '', length: 0, type: 'mismatch' };
+    const mismatchRecords = [];
+    const opsLength = ops.length;
+    const seqLength = seq.length;
+    const hasQual = qual !== undefined;
+    const cigarLength = cigarMismatches.length;
+    let hasSkips = false;
+    for (let k = 0; k < cigarLength; k++) {
+        if (cigarMismatches[k].type === 'skip') {
+            hasSkips = true;
+            break;
+        }
+    }
+    let currStart = 0;
     let lastCigar = 0;
     let lastTemplateOffset = 0;
     let lastRefOffset = 0;
     let lastSkipPos = 0;
-    const mismatchRecords = [];
-    const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
-    function nextRecord() {
-        mismatchRecords.push(curr);
-        curr = {
-            start: curr.start + curr.length,
-            length: 0,
-            base: '',
-            type: 'mismatch',
-        };
-    }
-    function getTemplateCoordLocal(refCoord) {
-        let templateOffset = lastTemplateOffset;
-        let refOffset = lastRefOffset;
-        for (let i = lastCigar; i < ops.length && refOffset <= refCoord; i += 2, lastCigar = i) {
-            const len = +ops[i];
-            const op = ops[i + 1];
-            if (op === 'S' || op === 'I') {
-                templateOffset += len;
-            }
-            else if (op === 'D' || op === 'P' || op === 'N') {
-                refOffset += len;
-            }
-            else if (op !== 'H') {
-                templateOffset += len;
-                refOffset += len;
+    let i = 0;
+    const len = mdstring.length;
+    while (i < len) {
+        const char = mdstring.charCodeAt(i);
+        if (char >= 48 && char <= 57) {
+            let num = 0;
+            while (i < len) {
+                const c = mdstring.charCodeAt(i);
+                if (c >= 48 && c <= 57) {
+                    num = num * 10 + (c - 48);
+                    i++;
+                }
+                else {
+                    break;
+                }
             }
+            currStart += num;
         }
-        lastTemplateOffset = templateOffset;
-        lastRefOffset = refOffset;
-        return templateOffset - (refOffset - refCoord);
-    }
-    const md = mdstring.match(mdRegex) || [];
-    for (const token of md) {
-        const num = +token;
-        if (!Number.isNaN(num)) {
-            curr.start += num;
-        }
-        else if (token.startsWith('^')) {
-            curr.start += token.length - 1;
+        else if (char === 94) {
+            i++;
+            let delLen = 0;
+            while (i < len) {
+                const c = mdstring.charCodeAt(i);
+                if (c >= 65 && c <= 90) {
+                    delLen++;
+                    i++;
+                }
+                else {
+                    break;
+                }
+            }
+            currStart += delLen;
         }
-        else {
-            for (let j = 0; j < token.length; j += 1) {
-                curr.length = 1;
-                while (lastSkipPos < skips.length) {
-                    const mismatch = skips[lastSkipPos];
-                    if (curr.start >= mismatch.start) {
-                        curr.start += mismatch.length;
+        else if (char >= 65 && char <= 90) {
+            const letter = mdstring[i];
+            i++;
+            if (hasSkips) {
+                while (lastSkipPos < cigarLength) {
+                    const mismatch = cigarMismatches[lastSkipPos];
+                    if (mismatch.type === 'skip' && currStart >= mismatch.start) {
+                        currStart += mismatch.length;
                         lastSkipPos++;
                     }
-                    else {
+                    else if (mismatch.type === 'skip') {
                         break;
                     }
+                    else {
+                        lastSkipPos++;
+                    }
                 }
-                const s = getTemplateCoordLocal(curr.start);
-                curr.base = seq[s] || 'X';
-                curr.qual = qual === null || qual === void 0 ? void 0 : qual[s];
-                curr.altbase = token;
-                nextRecord();
             }
+            let templateOffset = lastTemplateOffset;
+            let refOffset = lastRefOffset;
+            for (let j = lastCigar; j < opsLength && refOffset <= currStart; j += 2, lastCigar = j) {
+                const len = +ops[j];
+                const op = ops[j + 1];
+                if (op === 'S' || op === 'I') {
+                    templateOffset += len;
+                }
+                else if (op === 'D' || op === 'P' || op === 'N') {
+                    refOffset += len;
+                }
+                else if (op !== 'H') {
+                    templateOffset += len;
+                    refOffset += len;
+                }
+            }
+            lastTemplateOffset = templateOffset;
+            lastRefOffset = refOffset;
+            const s = templateOffset - (refOffset - currStart);
+            const base = s < seqLength ? seq[s] : 'X';
+            mismatchRecords.push({
+                start: currStart,
+                base,
+                qual: hasQual ? qual[s] : undefined,
+                altbase: letter,
+                length: 1,
+                type: 'mismatch',
+            });
+            currStart++;
+        }
+        else {
+            i++;
         }
     }
     return mismatchRecords;

package/esm/MismatchParser/mdToMismatches2.d.ts

@@ -0,0 +1,2 @@
+import type { Mismatch } from '../shared/types.ts';
+export declare function mdToMismatches2(mdstring: string, ops: Uint32Array | undefined, cigarMismatches: Mismatch[], seq: string, qual?: Uint8Array): Mismatch[];

package/esm/MismatchParser/mdToMismatches2.js

@@ -0,0 +1,96 @@
+import { CIGAR_D, CIGAR_H, CIGAR_I, CIGAR_N, CIGAR_P, CIGAR_S, } from "../PileupRenderer/renderers/cigarUtil.js";
+export function mdToMismatches2(mdstring, ops, cigarMismatches, seq, qual) {
+    if (!ops) {
+        return [];
+    }
+    const mismatchRecords = [];
+    const opsLength = ops.length;
+    const seqLength = seq.length;
+    const hasQual = qual !== undefined;
+    const cigarLength = cigarMismatches.length;
+    let hasSkips = false;
+    for (let k = 0; k < cigarLength; k++) {
+        if (cigarMismatches[k].type === 'skip') {
+            hasSkips = true;
+            break;
+        }
+    }
+    let currStart = 0;
+    let lastCigar = 0;
+    let lastTemplateOffset = 0;
+    let lastRefOffset = 0;
+    let lastSkipPos = 0;
+    let i = 0;
+    const len = mdstring.length;
+    while (i < len) {
+        const char = mdstring.charCodeAt(i);
+        if (char >= 48 && char <= 57) {
+            let num = 0;
+            while (i < len) {
+                const c = mdstring.charCodeAt(i);
+                if (c >= 48 && c <= 57) {
+                    num = num * 10 + (c - 48);
+                    i++;
+                }
+                else {
+                    break;
+                }
+            }
+            currStart += num;
+        }
+        else if (char === 94) {
+            i++;
+            while (i < len && mdstring.charCodeAt(i) >= 65) {
+                i++;
+                currStart++;
+            }
+        }
+        else if (char >= 65) {
+            const letter = mdstring[i];
+            i++;
+            if (hasSkips && cigarLength > 0) {
+                for (let k = lastSkipPos; k < cigarLength; k++) {
+                    const mismatch = cigarMismatches[k];
+                    if (mismatch.type === 'skip' && currStart >= mismatch.start) {
+                        currStart += mismatch.length;
+                        lastSkipPos = k;
+                    }
+                }
+            }
+            let templateOffset = lastTemplateOffset;
+            let refOffset = lastRefOffset;
+            for (let j = lastCigar; j < opsLength && refOffset <= currStart; j++, lastCigar = j) {
+                const packed = ops[j];
+                const len = packed >> 4;
+                const op = packed & 0xf;
+                if (op === CIGAR_S || op === CIGAR_I) {
+                    templateOffset += len;
+                }
+                else if (op === CIGAR_D || op === CIGAR_P || op === CIGAR_N) {
+                    refOffset += len;
+                }
+                else if (op !== CIGAR_H) {
+                    templateOffset += len;
+                    refOffset += len;
+                }
+            }
+            lastTemplateOffset = templateOffset;
+            lastRefOffset = refOffset;
+            const s = templateOffset - (refOffset - currStart);
+            const base = s < seqLength ? seq[s] : 'X';
+            mismatchRecords.push({
+                start: currStart,
+                base,
+                qual: hasQual ? qual[s] : undefined,
+                altbase: letter,
+                length: 1,
+                type: 'mismatch',
+            });
+            currStart++;
+        }
+        else {
+            i++;
+        }
+    }
+    return mismatchRecords;
+}

package/esm/ModificationParser/detectSimplexModifications.d.ts

@@ -1,4 +1,4 @@
-import type { ModificationType } from '../shared/types';
+import type { ModificationType } from '../shared/types.ts';
 type ModificationTypeList = readonly ModificationType[];
 export declare function detectSimplexModifications(modifications: ModificationTypeList): ReadonlySet<string>;
 export {};

package/esm/ModificationParser/getMethBins.d.ts

@@ -1,5 +1,5 @@
 import type { Feature } from '@jbrowse/core/util';
-export declare function getMethBins(feature: Feature, cigarOps: string[]): {
+export declare function getMethBins(feature: Feature, cigarOps: ArrayLike<number>): {
     methBins: number[];
     hydroxyMethBins: number[];
     methProbs: number[];

package/esm/ModificationParser/getMethBins.js

@@ -1,7 +1,7 @@
-import { getNextRefPos } from '../MismatchParser';
-import { getModPositions } from './getModPositions';
-import { getModProbabilities } from './getModProbabilities';
-import { getTagAlt } from '../util';
+import { getModPositions } from "./getModPositions.js";
+import { getModProbabilities } from "./getModProbabilities.js";
+import { getNextRefPos } from "../MismatchParser/index.js";
+import { getTagAlt } from "../util.js";
 export function getMethBins(feature, cigarOps) {
     const fstart = feature.get('start');
     const fend = feature.get('end');
@@ -24,7 +24,7 @@ export function getMethBins(feature, cigarOps) {
                 }
                 const isReverseStrand = fstrand === -1;
                 const idx2 = probIndex + (isReverseStrand ? positions.length - 1 - idx : idx);
-                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
+                const prob = probabilities?.[idx2] || 0;
                 if (type === 'm') {
                     methBins[ref] = 1;
                     methProbs[ref] = prob;

package/esm/ModificationParser/getModPositions.js

@@ -1,5 +1,5 @@
 import { revcom } from '@jbrowse/core/util';
-import { modificationRegex } from './consts';
+import { modificationRegex } from "./consts.js";
 export function getModPositions(mm, fseq, fstrand) {
     const seq = fstrand === -1 ? revcom(fseq) : fseq;
     const seqLength = seq.length;

package/esm/ModificationParser/getModProbabilities.js

@@ -1,4 +1,4 @@
-import { getTagAlt } from '../util';
+import { getTagAlt } from "../util.js";
 export function getModProbabilities(feature) {
     const m = getTagAlt(feature, 'ML', 'Ml') || [];
     if (m) {

package/esm/ModificationParser/getModTypes.js

@@ -1,4 +1,4 @@
-import { modificationRegex } from './consts';
+import { modificationRegex } from "./consts.js";
 export function getModTypes(mm) {
     const result = [];
     const mods = mm.split(';');

package/esm/PileupRPC/base.js

@@ -2,9 +2,8 @@ import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
 import { renameRegionsIfNeeded } from '@jbrowse/core/util';
 export default class PileupBaseRPC extends RpcMethodType {
     async serializeArguments(args, rpcDriver) {
-        var _a;
         const { rootModel } = this.pluginManager;
-        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        const assemblyManager = rootModel?.session?.assemblyManager;
         if (!assemblyManager) {
             throw new Error('no assembly manager available');
         }

package/esm/PileupRPC/index.js

@@ -1,6 +1,5 @@
-import { PileupGetGlobalValueForTag, PileupGetReducedFeatures, PileupGetVisibleModifications, } from './rpcMethods';
+import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, } from "./rpcMethods.js";
 export default function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));
-    pm.addRpcMethod(() => new PileupGetReducedFeatures(pm));
 }

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

@@ -1,4 +1,4 @@
-import PileupBaseRPC from '../base';
+import PileupBaseRPC from '../base.ts';
 import type { Region } from '@jbrowse/core/util';
 export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
     name: string;

package/esm/PileupRPC/methods/GetGlobalValueForTag.js

@@ -1,12 +1,9 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
-import PileupBaseRPC from '../base';
+import PileupBaseRPC from "../base.js";
 export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetGlobalValueForTag';
-    }
+    name = 'PileupGetGlobalValueForTag';
     async execute(args, rpcDriver) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
         const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
@@ -15,7 +12,7 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
         const featuresArray = await firstValueFrom(features.pipe(toArray()));
         return [
             ...new Set(featuresArray
-                .map(feature => { var _a; return (_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a[tag]; })
+                .map(feature => feature.get('tags')?.[tag])
                 .filter(f => f !== undefined)
                 .map(f => `${f}`)),
         ];

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

@@ -1,5 +1,5 @@
-import PileupBaseRPC from '../base';
-import type { ModificationType } from '../../shared/types';
+import PileupBaseRPC from '../base.ts';
+import type { ModificationType } from '../../shared/types.ts';
 import type { Region } from '@jbrowse/core/util';
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
     name: string;

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -1,15 +1,12 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
-import { detectSimplexModifications } from '../../ModificationParser/detectSimplexModifications';
-import { getModTypes } from '../../ModificationParser/getModTypes';
-import { getTagAlt } from '../../util';
-import PileupBaseRPC from '../base';
+import { detectSimplexModifications } from "../../ModificationParser/detectSimplexModifications.js";
+import { getModTypes } from "../../ModificationParser/getModTypes.js";
+import { getTagAlt } from "../../util.js";
+import PileupBaseRPC from "../base.js";
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetVisibleModifications';
-    }
+    name = 'PileupGetVisibleModifications';
     async execute(args, rpcDriver) {
         const deserializeArguments = await this.deserializeArguments(args, rpcDriver);
         const { adapterConfig, sessionId, regions } = deserializeArguments;

package/esm/PileupRPC/rpcMethods.d.ts

@@ -1,3 +1,2 @@
-export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
-export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
-export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';
+export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications.ts';
+export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag.ts';

package/esm/PileupRPC/rpcMethods.js

@@ -1,3 +1,2 @@
-export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
-export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
-export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';
+export { default as PileupGetVisibleModifications } from "./methods/GetVisibleModifications.js";
+export { default as PileupGetGlobalValueForTag } from "./methods/GetGlobalValueForTag.js";

package/esm/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,22 +1,22 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
-import type { FilterBy, SortedBy } from '../shared/types';
-import type { CachedLayout, LayoutSessionProps } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
-import type GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import type MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+import { MultiLayout, PileupLayout } from '@jbrowse/core/util/layouts';
+import type { FilterBy, SortedBy } from '../shared/types.ts';
+import type { LayoutSessionLike, LayoutSessionProps } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
 export interface PileupLayoutSessionProps extends LayoutSessionProps {
     filterBy: FilterBy;
     sortedBy: SortedBy;
     showSoftClip: boolean;
 }
-type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-interface CachedPileupLayout extends CachedLayout {
+type MyMultiLayout = MultiLayout<PileupLayout<unknown>, unknown>;
+interface CachedPileupLayout {
+    layout: MyMultiLayout;
     props: PileupLayoutSessionProps;
 }
-export declare class PileupLayoutSession extends LayoutSession {
+export declare class PileupLayoutSession implements LayoutSessionLike {
     props: PileupLayoutSessionProps;
     cachedLayout: CachedPileupLayout | undefined;
     constructor(props: PileupLayoutSessionProps);
-    update(props: PileupLayoutSessionProps): this;
+    update(props: LayoutSessionProps): this;
+    makeLayout(): MultiLayout<PileupLayout<unknown>, unknown>;
     cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
     get layout(): MyMultiLayout;
 }

package/esm/PileupRenderer/PileupLayoutSession.js

@@ -1,17 +1,30 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { MultiLayout, PileupLayout } from '@jbrowse/core/util/layouts';
 import deepEqual from 'fast-deep-equal';
-export class PileupLayoutSession extends LayoutSession {
+export class PileupLayoutSession {
+    props;
+    cachedLayout;
     constructor(props) {
-        super(props);
         this.props = props;
     }
     update(props) {
-        super.update(props);
         this.props = props;
         return this;
     }
+    makeLayout() {
+        const noSpacing = readConfObject(this.props.config, 'noSpacing');
+        const featureHeight = readConfObject(this.props.config, 'height');
+        const maxHeight = readConfObject(this.props.config, 'maxHeight');
+        return new MultiLayout(PileupLayout, {
+            featureHeight,
+            spacing: noSpacing ? 0 : 2,
+            maxHeight,
+        });
+    }
     cachedLayoutIsValid(cachedLayout) {
-        return (super.cachedLayoutIsValid(cachedLayout) &&
+        return (cachedLayout.props.bpPerPx === this.props.bpPerPx &&
+            deepEqual(readConfObject(this.props.config), readConfObject(cachedLayout.props.config)) &&
+            deepEqual(this.props.filters, cachedLayout.props.filters) &&
             this.props.showSoftClip === cachedLayout.props.showSoftClip &&
             deepEqual(this.props.sortedBy, cachedLayout.props.sortedBy) &&
             deepEqual(this.props.filterBy, cachedLayout.props.filterBy));

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -1,53 +1,11 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { PileupLayoutSession } from './PileupLayoutSession';
-import type { PileupLayoutSessionProps } from './PileupLayoutSession';
-import type { RenderArgsDeserialized } from './types';
+import { PileupLayoutSession } from './PileupLayoutSession.ts';
+import type { PileupLayoutSessionProps } from './PileupLayoutSession.ts';
+import type { RenderArgsDeserialized } from './types.ts';
 import type { Region } from '@jbrowse/core/util';
 export default class PileupRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    fetchSequence(renderProps: RenderArgsDeserialized, region: Region): Promise<any>;
-    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
-        start: number;
-        end: number;
-        refName: string;
-        reversed?: boolean | undefined;
-        assemblyName: string;
-    };
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<any, any>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        containsNoTransferables: boolean;
-        flatbush: ArrayBufferLike;
-        items: import("./types").FlatbushItem[];
-        reactElement: React.ReactElement;
-        html?: string;
-    }>;
+    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): Region;
+    render(renderProps: RenderArgsDeserialized): Promise<import("librpc-web-mod").RpcResult>;
     createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }