@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/MismatchParser/mdToMismatches.js

@@ -1,74 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.mdToMismatches = mdToMismatches;
-const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
-function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
-    let curr = { start: 0, base: '', length: 0, type: 'mismatch' };
-    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;
-            }
-        }
-        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 {
-            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;
-                        lastSkipPos++;
-                    }
-                    else {
-                        break;
-                    }
-                }
-                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();
-            }
-        }
-    }
-    return mismatchRecords;
-}

package/dist/ModificationParser/consts.d.ts

@@ -1 +0,0 @@
-export declare const modificationRegex: RegExp;

package/dist/ModificationParser/consts.js

@@ -1,4 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationRegex = void 0;
-exports.modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);

package/dist/ModificationParser/detectSimplexModifications.d.ts

@@ -1,4 +0,0 @@
-import type { ModificationType } from '../shared/types';
-type ModificationTypeList = readonly ModificationType[];
-export declare function detectSimplexModifications(modifications: ModificationTypeList): ReadonlySet<string>;
-export {};

package/dist/ModificationParser/detectSimplexModifications.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.detectSimplexModifications = detectSimplexModifications;
-function detectSimplexModifications(modifications) {
-    const minusStrandMods = new Set();
-    const simplexModifications = new Set();
-    for (const modification of modifications) {
-        const mod = modification;
-        if (mod.strand === '-') {
-            minusStrandMods.add(mod.type);
-        }
-    }
-    for (const modification of modifications) {
-        const mod = modification;
-        if (mod.strand === '+' && !minusStrandMods.has(mod.type)) {
-            simplexModifications.add(mod.type);
-        }
-    }
-    return simplexModifications;
-}

package/dist/ModificationParser/getMethBins.d.ts

@@ -1,7 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getMethBins(feature: Feature, cigarOps: string[]): {
-    methBins: number[];
-    hydroxyMethBins: number[];
-    methProbs: number[];
-    hydroxyMethProbs: number[];
-};

package/dist/ModificationParser/getMethBins.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMethBins = getMethBins;
-const MismatchParser_1 = require("../MismatchParser");
-const getModPositions_1 = require("./getModPositions");
-const getModProbabilities_1 = require("./getModProbabilities");
-const util_1 = require("../util");
-function getMethBins(feature, cigarOps) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const flen = fend - fstart;
-    const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-    const methBins = [];
-    const hydroxyMethBins = [];
-    const methProbs = [];
-    const hydroxyMethProbs = [];
-    const seq = feature.get('seq');
-    if (seq) {
-        const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
-        const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
-        let probIndex = 0;
-        for (const { type, positions } of modifications) {
-            for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
-                if (ref < 0 || ref >= flen) {
-                    continue;
-                }
-                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;
-                if (type === 'm') {
-                    methBins[ref] = 1;
-                    methProbs[ref] = prob;
-                }
-                else if (type === 'h') {
-                    hydroxyMethBins[ref] = 1;
-                    hydroxyMethProbs[ref] = prob;
-                }
-            }
-            probIndex += positions.length;
-        }
-    }
-    return {
-        methBins,
-        hydroxyMethBins,
-        methProbs,
-        hydroxyMethProbs,
-    };
-}

package/dist/ModificationParser/getModPositions.d.ts

@@ -1,6 +0,0 @@
-export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
-    type: string;
-    base: string;
-    strand: string;
-    positions: any[];
-}[];

package/dist/ModificationParser/getModPositions.js

@@ -1,61 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModPositions = getModPositions;
-const util_1 = require("@jbrowse/core/util");
-const consts_1 = require("./consts");
-function getModPositions(mm, fseq, fstrand) {
-    const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
-    const seqLength = seq.length;
-    const mods = mm.split(';');
-    const result = [];
-    for (const mod of mods) {
-        if (mod === '') {
-            continue;
-        }
-        const split = mod.split(',');
-        const basemod = split[0];
-        const matches = consts_1.modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error(`bad format for MM tag: "${mod}"`);
-        }
-        const [, base, strand, typestr] = matches;
-        const types = typestr.split(/(\d+|.)/);
-        for (const type of types) {
-            if (type === '') {
-                continue;
-            }
-            const splitLength = split.length;
-            let currPos = 0;
-            const positions = fstrand === -1 ? new Array(splitLength - 1) : [];
-            let writeIndex = fstrand === -1 ? splitLength - 2 : 0;
-            for (let i = 1; i < splitLength; i++) {
-                let delta = +split[i];
-                do {
-                    if (base === 'N' || base === seq[currPos]) {
-                        delta--;
-                    }
-                    currPos++;
-                } while (delta >= 0 && currPos < seqLength);
-                if (fstrand === -1) {
-                    const pos = seqLength - currPos;
-                    if (pos >= 0) {
-                        positions[writeIndex--] = pos;
-                    }
-                    else {
-                    }
-                }
-                else {
-                    positions[writeIndex++] = currPos - 1;
-                }
-            }
-            const validPositions = fstrand === -1 ? positions.slice(writeIndex + 1) : positions;
-            result.push({
-                type,
-                base: base,
-                strand: strand,
-                positions: validPositions,
-            });
-        }
-    }
-    return result;
-}

package/dist/ModificationParser/getModProbabilities.d.ts

@@ -1,2 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getModProbabilities(feature: Feature): number[] | undefined;

package/dist/ModificationParser/getModProbabilities.js

@@ -1,34 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModProbabilities = getModProbabilities;
-const util_1 = require("../util");
-function getModProbabilities(feature) {
-    const m = (0, util_1.getTagAlt)(feature, 'ML', 'Ml') || [];
-    if (m) {
-        const result = [];
-        if (typeof m === 'string') {
-            const parts = m.split(',');
-            for (let i = 0, l = parts.length; i < l; i++) {
-                result.push(+parts[i] / 255);
-            }
-        }
-        else {
-            for (let i = 0, l = m.length; i < l; i++) {
-                result.push(m[i] / 255);
-            }
-        }
-        return result;
-    }
-    else {
-        const mp = (0, util_1.getTagAlt)(feature, 'MP', 'Mp');
-        if (mp) {
-            const result = [];
-            for (let i = 0, l = mp.length; i < l; i++) {
-                const phred = mp.charCodeAt(i) - 33;
-                result.push(Math.min(1, phred / 50));
-            }
-            return result;
-        }
-        return undefined;
-    }
-}

package/dist/ModificationParser/getModTypes.d.ts

@@ -1,5 +0,0 @@
-export declare function getModTypes(mm: string): {
-    type: string;
-    base: string;
-    strand: string;
-}[];

package/dist/ModificationParser/getModTypes.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModTypes = getModTypes;
-const consts_1 = require("./consts");
-function getModTypes(mm) {
-    const result = [];
-    const mods = mm.split(';');
-    for (let i = 0, modsLen = mods.length; i < modsLen; i++) {
-        const mod = mods[i];
-        if (mod === '') {
-            continue;
-        }
-        const basemod = mod.split(',')[0];
-        const matches = consts_1.modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error(`bad format for MM tag: "${mod}"`);
-        }
-        const base = matches[1];
-        const strand = matches[2];
-        const typestr = matches[3];
-        const types = typestr.split(/(\d+|.)/);
-        for (let j = 0, typesLen = types.length; j < typesLen; j++) {
-            const type = types[j];
-            if (type === '') {
-                continue;
-            }
-            result.push({
-                type,
-                base,
-                strand,
-            });
-        }
-    }
-    return result;
-}

package/dist/PileupRPC/base.d.ts

@@ -1,8 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-export default abstract class PileupBaseRPC extends RpcMethodType {
-    serializeArguments(args: RenderArgs & {
-        stopToken?: string;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriver: string): Promise<Record<string, unknown>>;
-}

package/dist/PileupRPC/base.js

@@ -1,20 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-const util_1 = require("@jbrowse/core/util");
-class PileupBaseRPC extends RpcMethodType_1.default {
-    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;
-        if (!assemblyManager) {
-            throw new Error('no assembly manager available');
-        }
-        const renamedArgs = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, args);
-        return super.serializeArguments(renamedArgs, rpcDriver);
-    }
-}
-exports.default = PileupBaseRPC;

package/dist/PileupRPC/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function PileupRPCMethodsF(pm: PluginManager): void;

package/dist/PileupRPC/index.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = PileupRPCMethodsF;
-const rpcMethods_1 = require("./rpcMethods");
-function PileupRPCMethodsF(pm) {
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
-}

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

@@ -1,13 +0,0 @@
-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>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<string[]>;
-}

package/dist/PileupRPC/methods/GetGlobalValueForTag.js

@@ -1,29 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const base_1 = __importDefault(require("../base"));
-class PileupGetGlobalValueForTag extends base_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetGlobalValueForTag';
-    }
-    async execute(args, rpcDriver) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions, deserializedArgs);
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
-        return [
-            ...new Set(featuresArray
-                .map(feature => { var _a; return (_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a[tag]; })
-                .filter(f => f !== undefined)
-                .map(f => `${f}`)),
-        ];
-    }
-}
-exports.default = PileupGetGlobalValueForTag;

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

@@ -1,37 +0,0 @@
-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>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<{
-        chains: {
-            id: string;
-            refName: string;
-            name: any;
-            start: number;
-            strand: any;
-            end: number;
-            flags: any;
-            tlen: any;
-            pair_orientation: any;
-            next_ref: any;
-            next_pos: any;
-            clipPos: number;
-            SA: any;
-        }[][];
-        stats: {
-            upper: number;
-            lower: number;
-            avg: number;
-            sd: number;
-        } | undefined;
-        hasPaired: boolean;
-        containsNoTransferables: boolean;
-    }>;
-}

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -1,54 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const util_1 = require("@jbrowse/core/util");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const MismatchParser_1 = require("../../MismatchParser");
-const base_1 = __importDefault(require("../base"));
-const util_2 = require("../util");
-class PileupGetReducedFeatures extends base_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetReducedFeatures';
-    }
-    async execute(args, rpcDriver) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe((0, operators_1.toArray)()));
-        const reduced = (0, util_1.dedupe)(featuresArray.map(f => {
-            var _a;
-            return ({
-                id: f.id(),
-                refName: f.get('refName'),
-                name: f.get('name'),
-                start: f.get('start'),
-                strand: f.get('strand'),
-                end: f.get('end'),
-                flags: f.get('flags'),
-                tlen: f.get('template_length'),
-                pair_orientation: f.get('pair_orientation'),
-                next_ref: f.get('next_ref'),
-                next_pos: f.get('next_pos'),
-                clipPos: (0, MismatchParser_1.getClip)(f.get('CIGAR'), f.get('strand')),
-                SA: (_a = f.get('tags')) === null || _a === void 0 ? void 0 : _a.SA,
-            });
-        }), f => f.id);
-        const filtered = (0, util_2.filterForPairs)(reduced);
-        const stats = filtered.length ? (0, util_2.getInsertSizeStats)(filtered) : undefined;
-        const chains = (0, util_1.groupBy)(reduced, f => f.name);
-        return {
-            chains: Object.values(chains),
-            stats,
-            hasPaired: !!stats,
-            containsNoTransferables: true,
-        };
-    }
-}
-exports.default = PileupGetReducedFeatures;

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

@@ -1,17 +0,0 @@
-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>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<{
-        modifications: ModificationType[];
-        simplexModifications: string[];
-    }>;
-}

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -1,49 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const detectSimplexModifications_1 = require("../../ModificationParser/detectSimplexModifications");
-const getModTypes_1 = require("../../ModificationParser/getModTypes");
-const util_1 = require("../../util");
-const base_1 = __importDefault(require("../base"));
-class PileupGetVisibleModifications extends base_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetVisibleModifications';
-    }
-    async execute(args, rpcDriver) {
-        const deserializeArguments = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = deserializeArguments;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializeArguments)
-            .pipe((0, operators_1.toArray)()));
-        const uniqueModifications = new Map();
-        for (const feat of featuresArray) {
-            const mmTag = (0, util_1.getTagAlt)(feat, 'MM', 'Mm');
-            for (const mod of (0, getModTypes_1.getModTypes)(typeof mmTag === 'string' ? mmTag : '')) {
-                const key = `${mod.base}${mod.strand}${mod.type}`;
-                if (!uniqueModifications.has(key)) {
-                    uniqueModifications.set(key, mod);
-                }
-            }
-        }
-        const modifications = [...uniqueModifications.values()];
-        const simplexModifications = (0, detectSimplexModifications_1.detectSimplexModifications)(modifications);
-        const modificationsForDisplay = new Map();
-        for (const mod of modifications) {
-            if (!modificationsForDisplay.has(mod.type)) {
-                modificationsForDisplay.set(mod.type, mod);
-            }
-        }
-        return {
-            modifications: [...modificationsForDisplay.values()],
-            simplexModifications: [...simplexModifications],
-        };
-    }
-}
-exports.default = PileupGetVisibleModifications;

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,3 +0,0 @@
-export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
-export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
-export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';

package/dist/PileupRPC/rpcMethods.js

@@ -1,12 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PileupGetGlobalValueForTag = exports.PileupGetVisibleModifications = exports.PileupGetReducedFeatures = void 0;
-var GetReducedFeatures_1 = require("./methods/GetReducedFeatures");
-Object.defineProperty(exports, "PileupGetReducedFeatures", { enumerable: true, get: function () { return __importDefault(GetReducedFeatures_1).default; } });
-var GetVisibleModifications_1 = require("./methods/GetVisibleModifications");
-Object.defineProperty(exports, "PileupGetVisibleModifications", { enumerable: true, get: function () { return __importDefault(GetVisibleModifications_1).default; } });
-var GetGlobalValueForTag_1 = require("./methods/GetGlobalValueForTag");
-Object.defineProperty(exports, "PileupGetGlobalValueForTag", { enumerable: true, get: function () { return __importDefault(GetGlobalValueForTag_1).default; } });

package/dist/PileupRPC/util.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getInsertSizeStats = getInsertSizeStats;
-exports.filterForPairs = filterForPairs;
-function getInsertSizeStats(features) {
-    const filtered = features.map(f => Math.abs(f.tlen));
-    const sum = filtered.reduce((a, b) => a + b, 0);
-    const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0);
-    const total = filtered.length;
-    const avg = sum / total;
-    const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total));
-    const upper = avg + 4 * sd;
-    const lower = avg - 3 * sd;
-    return { upper, lower, avg, sd };
-}
-function filterForPairs(features) {
-    return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
-}

package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,23 +0,0 @@
-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';
-export interface PileupLayoutSessionProps extends LayoutSessionProps {
-    filterBy: FilterBy;
-    sortedBy: SortedBy;
-    showSoftClip: boolean;
-}
-type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-interface CachedPileupLayout extends CachedLayout {
-    props: PileupLayoutSessionProps;
-}
-export declare class PileupLayoutSession extends LayoutSession {
-    props: PileupLayoutSessionProps;
-    cachedLayout: CachedPileupLayout | undefined;
-    constructor(props: PileupLayoutSessionProps);
-    update(props: PileupLayoutSessionProps): this;
-    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
-    get layout(): MyMultiLayout;
-}
-export {};