@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -1,89 +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 BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const rxjs_2 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const util_1 = require("../util");
-const generateCoverageBins_1 = require("./generateCoverageBins");
-class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configure() {
-        var _a, _b;
-        const subadapterConfig = this.getConf('subadapter');
-        const sequenceConf = subadapterConfig.sequenceAdapter;
-        const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig));
-        const sequenceAdapter = sequenceConf
-            ? await ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))
-            : undefined;
-        if (!dataAdapter) {
-            throw new Error('Failed to get subadapter');
-        }
-        return {
-            subadapter: dataAdapter.dataAdapter,
-            sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter,
-        };
-    }
-    async fetchSequence(region) {
-        const { sequenceAdapter } = await this.configure();
-        if (!sequenceAdapter) {
-            return undefined;
-        }
-        return (0, util_1.fetchSequence)(region, sequenceAdapter);
-    }
-    getFeatures(region, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { subadapter } = await this.configure();
-            const features = await (0, rxjs_2.firstValueFrom)(subadapter.getFeatures(region, opts).pipe((0, operators_1.toArray)()));
-            const { bins, skipmap } = await (0, generateCoverageBins_1.generateCoverageBins)({
-                features,
-                region,
-                opts,
-                fetchSequence: (region) => this.fetchSequence(region),
-            });
-            let index = 0;
-            for (const bin of bins) {
-                if (bin) {
-                    const start = region.start + index;
-                    observer.next(new simpleFeature_1.default({
-                        id: `${this.id}-${start}`,
-                        data: {
-                            score: bin.depth,
-                            snpinfo: bin,
-                            start,
-                            end: start + 1,
-                            refName: region.refName,
-                        },
-                    }));
-                }
-                index++;
-            }
-            for (const [key, skip] of Object.entries(skipmap)) {
-                observer.next(new simpleFeature_1.default({
-                    id: key,
-                    data: {
-                        type: 'skip',
-                        start: skip.start,
-                        end: skip.end,
-                        strand: skip.strand,
-                        score: skip.score,
-                        effectiveStrand: skip.effectiveStrand,
-                    },
-                }));
-            }
-            observer.complete();
-        }, opts.stopToken);
-    }
-    async getMultiRegionFeatureDensityStats(regions, opts) {
-        const { subadapter } = await this.configure();
-        return subadapter.getMultiRegionFeatureDensityStats(regions, opts);
-    }
-    async getRefNames(opts = {}) {
-        const { subadapter } = await this.configure();
-        return subadapter.getRefNames(opts);
-    }
-}
-exports.default = SNPCoverageAdapter;

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,7 +0,0 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    subadapter: {
-        type: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default configSchema;

package/dist/SNPCoverageAdapter/configSchema.js

@@ -1,11 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
-    subadapter: {
-        type: 'frozen',
-        defaultValue: null,
-    },
-}, { explicitlyTyped: true });
-exports.default = configSchema;

package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,13 +0,0 @@
-import type { Opts } from './util';
-import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-export declare function generateCoverageBins({ fetchSequence, features, region, opts, }: {
-    features: Feature[];
-    region: Region;
-    opts: Opts;
-    fetchSequence: (arg: Region) => Promise<string>;
-}): Promise<{
-    bins: PreBaseCoverageBin[];
-    skipmap: SkipMap;
-}>;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,87 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateCoverageBins = generateCoverageBins;
-const util_1 = require("@jbrowse/core/util");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const processDepth_1 = require("./processDepth");
-const processMismatches_1 = require("./processMismatches");
-const processModifications_1 = require("./processModifications");
-const processReferenceCpGs_1 = require("./processReferenceCpGs");
-async function generateCoverageBins({ fetchSequence, features, region, opts, }) {
-    const { stopToken, colorBy } = opts;
-    const skipmap = {};
-    const bins = [];
-    const start2 = Math.max(0, region.start - 1);
-    const diff = region.start - start2;
-    let regionSequence;
-    let start = performance.now();
-    for (const feature of features) {
-        if (performance.now() - start > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            start = performance.now();
-        }
-        (0, processDepth_1.processDepth)({
-            feature,
-            bins,
-            region,
-        });
-        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '');
-            (0, processModifications_1.processModifications)({
-                feature,
-                colorBy,
-                bins,
-                region,
-                regionSequence: regionSequence.slice(diff),
-            });
-        }
-        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '');
-            (0, processReferenceCpGs_1.processReferenceCpGs)({
-                feature,
-                bins,
-                region,
-                regionSequence,
-            });
-        }
-        (0, processMismatches_1.processMismatches)({ feature, skipmap, bins, region });
-    }
-    for (const bin of bins) {
-        if (bin) {
-            bin.mods = Object.fromEntries(Object.entries(bin.mods).map(([key, val]) => {
-                return [
-                    key,
-                    {
-                        ...val,
-                        avgProbability: val.probabilities.length
-                            ? (0, util_1.sum)(val.probabilities) / val.probabilities.length
-                            : undefined,
-                    },
-                ];
-            }));
-            bin.nonmods = Object.fromEntries(Object.entries(bin.nonmods).map(([key, val]) => {
-                return [
-                    key,
-                    {
-                        ...val,
-                        avgProbability: val.probabilities.length
-                            ? (0, util_1.sum)(val.probabilities) / val.probabilities.length
-                            : undefined,
-                    },
-                ];
-            }));
-        }
-    }
-    return {
-        bins,
-        skipmap,
-    };
-}

package/dist/SNPCoverageAdapter/index.d.ts

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

package/dist/SNPCoverageAdapter/index.js

@@ -1,54 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SNPCoverageAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function SNPCoverageAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'SNPCoverageAdapter',
-            displayName: 'SNPCoverage adapter',
-            adapterMetadata: {
-                hiddenFromGUI: true,
-            },
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
-            configSchema: configSchema_1.default,
-        });
-    });
-}

package/dist/SNPCoverageAdapter/processDepth.d.ts

@@ -1,8 +0,0 @@
-import type { PreBaseCoverageBin } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion } from '@jbrowse/core/util/types';
-export declare function processDepth({ feature, bins, region, }: {
-    feature: Feature;
-    bins: PreBaseCoverageBin[];
-    region: AugmentedRegion;
-}): void;

package/dist/SNPCoverageAdapter/processDepth.js

@@ -1,38 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.processDepth = processDepth;
-function processDepth({ feature, bins, region, }) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const regionLength = region.end - region.start;
-    for (let j = fstart; j < fend + 1; j++) {
-        const i = j - region.start;
-        if (i >= 0 && i < regionLength) {
-            if (bins[i] === undefined) {
-                bins[i] = {
-                    depth: 0,
-                    readsCounted: 0,
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    snps: {},
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            if (j !== fend) {
-                bins[i].depth++;
-                bins[i].readsCounted++;
-                bins[i].ref.entryDepth++;
-                bins[i].ref[fstrand]++;
-            }
-        }
-    }
-}

package/dist/SNPCoverageAdapter/processMismatches.d.ts

@@ -1,9 +0,0 @@
-import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion } from '@jbrowse/core/util/types';
-export declare function processMismatches({ feature, region, bins, skipmap, }: {
-    region: AugmentedRegion;
-    bins: PreBaseCoverageBin[];
-    feature: Feature;
-    skipmap: SkipMap;
-}): void;

package/dist/SNPCoverageAdapter/processMismatches.js

@@ -1,58 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.processMismatches = processMismatches;
-const util_1 = require("./util");
-function processMismatches({ feature, region, bins, skipmap, }) {
-    var _a;
-    const fstart = feature.get('start');
-    const fstrand = feature.get('strand');
-    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
-    for (const mismatch of mismatches) {
-        const mstart = fstart + mismatch.start;
-        const mlen = (0, util_1.mismatchLen)(mismatch);
-        const mend = mstart + mlen;
-        for (let j = mstart; j < mstart + mlen; j++) {
-            const epos = j - region.start;
-            if (epos >= 0 && epos < bins.length) {
-                const bin = bins[epos];
-                const { base, altbase, type } = mismatch;
-                const interbase = (0, util_1.isInterbase)(type);
-                if (type === 'deletion' || type === 'skip') {
-                    (0, util_1.inc)(bin, fstrand, 'delskips', type);
-                    bin.depth--;
-                }
-                else if (!interbase) {
-                    (0, util_1.inc)(bin, fstrand, 'snps', base);
-                    bin.ref.entryDepth--;
-                    bin.ref[fstrand]--;
-                    bin.refbase = altbase;
-                }
-                else {
-                    (0, util_1.inc)(bin, fstrand, 'noncov', type);
-                }
-            }
-        }
-        if (mismatch.type === 'skip') {
-            const tags = feature.get('tags');
-            const xs = (tags === null || tags === void 0 ? void 0 : tags.XS) || (tags === null || tags === void 0 ? void 0 : tags.TS);
-            const ts = tags === null || tags === void 0 ? void 0 : tags.ts;
-            const effectiveStrand = xs === '+'
-                ? 1
-                : xs === '-'
-                    ? -1
-                    : (ts === '+' ? 1 : xs === '-' ? -1 : 0) * fstrand;
-            const hash = `${mstart}_${mend}_${effectiveStrand}`;
-            if (skipmap[hash] === undefined) {
-                skipmap[hash] = {
-                    feature: feature,
-                    start: mstart,
-                    end: mend,
-                    strand: fstrand,
-                    effectiveStrand,
-                    score: 0,
-                };
-            }
-            skipmap[hash].score++;
-        }
-    }
-}

package/dist/SNPCoverageAdapter/processModifications.d.ts

@@ -1,10 +0,0 @@
-import type { ColorBy, PreBaseCoverageBin } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-export declare function processModifications({ feature, colorBy, region, bins, regionSequence, }: {
-    bins: PreBaseCoverageBin[];
-    feature: Feature;
-    region: Region;
-    colorBy?: ColorBy;
-    regionSequence: string;
-}): void;

package/dist/SNPCoverageAdapter/processModifications.js

@@ -1,60 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.processModifications = processModifications;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const MismatchParser_1 = require("../MismatchParser");
-const getMaximumModificationAtEachPosition_1 = require("../shared/getMaximumModificationAtEachPosition");
-function processModifications({ feature, colorBy, region, bins, regionSequence, }) {
-    var _a, _b, _c, _d, _e;
-    const fstart = feature.get('start');
-    const fstrand = feature.get('strand');
-    const fend = feature.get('end');
-    const twoColor = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.twoColor;
-    const isolatedModification = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.isolatedModification;
-    const seq = feature.get('seq');
-    const modificationThreshold = (_d = (_c = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _c === void 0 ? void 0 : _c.threshold) !== null && _d !== void 0 ? _d : 10;
-    const thresholdFraction = modificationThreshold / 100;
-    if (!seq) {
-        return;
-    }
-    const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-    (_e = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature, cigarOps)) === null || _e === void 0 ? void 0 : _e.forEach(({ allProbs, prob, type }, pos) => {
-        if (isolatedModification && type !== isolatedModification) {
-            return;
-        }
-        if (prob < thresholdFraction) {
-            return;
-        }
-        const epos = pos + fstart - region.start;
-        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-            if (bins[epos] === undefined) {
-                bins[epos] = {
-                    depth: 0,
-                    readsCounted: 0,
-                    snps: {},
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            const bin = bins[epos];
-            bin.refbase = regionSequence[epos];
-            const s = 1 - (0, util_1.sum)(allProbs);
-            if (twoColor && s > (0, util_1.max)(allProbs)) {
-                (0, util_2.incWithProbabilities)(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
-            }
-            else {
-                (0, util_2.incWithProbabilities)(bin, fstrand, 'mods', `mod_${type}`, prob);
-            }
-        }
-    });
-}

package/dist/SNPCoverageAdapter/processReferenceCpGs.d.ts

@@ -1,9 +0,0 @@
-import type { PreBaseCoverageBin } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-export declare function processReferenceCpGs({ feature, region, bins, regionSequence, }: {
-    bins: PreBaseCoverageBin[];
-    feature: Feature;
-    region: Region;
-    regionSequence: string;
-}): void;

package/dist/SNPCoverageAdapter/processReferenceCpGs.js

@@ -1,63 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.processReferenceCpGs = processReferenceCpGs;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
-const util_2 = require("./util");
-const getMethBins_1 = require("../ModificationParser/getMethBins");
-function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
-    var _a;
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const seq = feature.get('seq');
-    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
-    const r = regionSequence.toLowerCase();
-    if (seq) {
-        const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-        const { methBins, methProbs } = (0, getMethBins_1.getMethBins)(feature, cigarOps);
-        const dels = mismatches.filter(f => f.type === 'deletion');
-        for (let i = 0; i < fend - fstart; i++) {
-            const j = i + fstart;
-            const l1 = r[j - region.start + 1];
-            const l2 = r[j - region.start + 2];
-            if (l1 === 'c' && l2 === 'g') {
-                const bin0 = bins[j - region.start];
-                const bin1 = bins[j - region.start + 1];
-                const b0 = methBins[i];
-                const b1 = methBins[i + 1];
-                const p0 = methProbs[i];
-                const p1 = methProbs[i + 1];
-                if ((b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||
-                    (b1 && (p1 !== undefined ? p1 > 0.5 : true))) {
-                    if (bin0) {
-                        (0, util_2.incWithProbabilities)(bin0, fstrand, 'mods', 'cpg_meth', p0 || 0);
-                        bin0.ref.entryDepth--;
-                        bin0.ref[fstrand]--;
-                    }
-                    if (bin1) {
-                        (0, util_2.incWithProbabilities)(bin1, fstrand, 'mods', 'cpg_meth', p1 || 0);
-                        bin1.ref.entryDepth--;
-                        bin1.ref[fstrand]--;
-                    }
-                }
-                else {
-                    if (bin0) {
-                        if (!dels.some(d => (0, util_1.doesIntersect2)(j, j + 1, d.start + fstart, d.start + fstart + d.length))) {
-                            (0, util_2.incWithProbabilities)(bin0, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p0 || 0));
-                            bin0.ref.entryDepth--;
-                            bin0.ref[fstrand]--;
-                        }
-                    }
-                    if (bin1) {
-                        if (!dels.some(d => (0, util_1.doesIntersect2)(j + 1, j + 2, d.start + fstart, d.start + fstart + d.length))) {
-                            (0, util_2.incWithProbabilities)(bin1, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p1 || 0));
-                            bin1.ref.entryDepth--;
-                            bin1.ref[fstrand]--;
-                        }
-                    }
-                }
-            }
-        }
-    }
-}

package/dist/SNPCoverageAdapter/util.d.ts

@@ -1,10 +0,0 @@
-import type { ColorBy, Mismatch, PreBaseCoverageBin, PreBaseCoverageBinSubtypes } from '../shared/types';
-export interface Opts {
-    bpPerPx?: number;
-    colorBy?: ColorBy;
-    stopToken?: string;
-}
-export declare function mismatchLen(mismatch: Mismatch): number;
-export declare function isInterbase(type: string): type is "insertion" | "hardclip" | "softclip";
-export declare function inc(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string): void;
-export declare function incWithProbabilities(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string, probability: number): void;

package/dist/SNPCoverageAdapter/util.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.mismatchLen = mismatchLen;
-exports.isInterbase = isInterbase;
-exports.inc = inc;
-exports.incWithProbabilities = incWithProbabilities;
-function mismatchLen(mismatch) {
-    return !isInterbase(mismatch.type) ? mismatch.length : 1;
-}
-function isInterbase(type) {
-    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
-}
-function inc(bin, strand, type, field) {
-    let thisBin = bin[type][field];
-    if (thisBin === undefined) {
-        thisBin = bin[type][field] = {
-            entryDepth: 0,
-            probabilities: [],
-            '-1': 0,
-            '0': 0,
-            '1': 0,
-        };
-    }
-    thisBin.entryDepth++;
-    thisBin[strand]++;
-}
-function incWithProbabilities(bin, strand, type, field, probability) {
-    let thisBin = bin[type][field];
-    if (thisBin === undefined) {
-        thisBin = bin[type][field] = {
-            entryDepth: 0,
-            probabilities: [],
-            '-1': 0,
-            '0': 0,
-            '1': 0,
-        };
-    }
-    thisBin.entryDepth++;
-    thisBin.probabilities.push(probability);
-    thisBin[strand]++;
-}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,5 +0,0 @@
-import { WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
-import type { RenderArgsDeserializedWithFeatures } from './types';
-export default class SNPCoverageRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
-}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,46 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("@jbrowse/core/util");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
-    async draw(ctx, props) {
-        const { statusCallback = () => { } } = props;
-        const { makeImage } = await Promise.resolve().then(() => __importStar(require('./makeImage')));
-        await (0, util_1.updateStatus)('Rendering coverage', statusCallback, () => makeImage(ctx, props));
-        return undefined;
-    }
-}
-exports.default = SNPCoverageRenderer;