@jbrowse/plugin-comparative-adapters 2.6.1

package/dist/PAFAdapter/SyntenyFeature.d.ts

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+import { SimpleFeature } from '@jbrowse/core/util';
+export default class SyntenyFeature extends SimpleFeature {
+    get(arg: string): any;
+}

package/dist/PAFAdapter/SyntenyFeature.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const util_1 = require("@jbrowse/core/util");
+const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
+// locals
+const { getMismatches } = plugin_alignments_1.MismatchParser;
+class SyntenyFeature extends util_1.SimpleFeature {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    get(arg) {
+        if (arg === 'mismatches') {
+            return getMismatches(this.get('CIGAR'));
+        }
+        return super.get(arg);
+    }
+}
+exports.default = SyntenyFeature;
+//# sourceMappingURL=SyntenyFeature.js.map

package/dist/PAFAdapter/SyntenyFeature.js.map

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+{"version":3,"file":"SyntenyFeature.js","sourceRoot":"","sources":["../../src/PAFAdapter/SyntenyFeature.ts"],"names":[],"mappings":";;AAAA,6CAAkD;AAClD,kEAA2D;AAE3D,SAAS;AACT,MAAM,EAAE,aAAa,EAAE,GAAG,kCAAc,CAAA;AAExC,MAAqB,cAAe,SAAQ,oBAAa;IACvD,8DAA8D;IAC9D,GAAG,CAAC,GAAW;QACb,IAAI,GAAG,KAAK,YAAY,EAAE;YACxB,OAAO,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;SACxC;QACD,OAAO,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IACvB,CAAC;CACF;AARD,iCAQC"}

package/dist/PAFAdapter/configSchema.d.ts

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+declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    targetAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    queryAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    pafLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PAFAdapter;

package/dist/PAFAdapter/configSchema.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config PAFAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const PAFAdapter = (0, configuration_1.ConfigurationSchema)('PAFAdapter', {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
+    },
+    /**
+     * #slot
+     */
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames: the target assembly name',
+    },
+    /**
+     * #slot
+     */
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames: the query assembly name',
+    },
+    /**
+     * #slot
+     */
+    pafLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/file.paf',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+exports.default = PAFAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/PAFAdapter/configSchema.js.map

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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PAFAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,GAAG,IAAA,mCAAmB,EACpC,YAAY,EACZ;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,2IAA2I;KAC9I;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,wDAAwD;KACtE;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,mBAAmB;YACxB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,UAAU,CAAA"}

package/dist/PAFAdapter/index.d.ts

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+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/PAFAdapter/index.js

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+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 });
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'PAFAdapter',
+        displayName: 'PAF adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PAFAdapter'))).then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/dist/PAFAdapter/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PAFAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,aAAa;QAC1B,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/PAFAdapter/util.d.ts

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+export interface PAFRecord {
+    qname: string;
+    qstart: number;
+    qend: number;
+    tname: string;
+    tstart: number;
+    tend: number;
+    strand: number;
+    extra: {
+        cg?: string;
+        blockLen?: number;
+        mappingQual: number;
+        numMatches?: number;
+        meanScore?: number;
+    };
+}
+export declare function getWeightedMeans(ret: PAFRecord[]): PAFRecord[];
+export declare function parsePAFLine(line: string): PAFRecord;
+export declare function flipCigar(cigar: string[]): string[];
+export declare function swapIndelCigar(cigar: string): string;

package/dist/PAFAdapter/util.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.swapIndelCigar = exports.flipCigar = exports.parsePAFLine = exports.getWeightedMeans = void 0;
+const util_1 = require("../util");
+// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
+// License reproduced here
+//
+// MIT License
+// Copyright (c) 2017 Tom Poorten
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+// The above copyright notice and this permission notice shall be included in all
+// copies or substantial portions of the Software.
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+//
+// Notes: in the weighted mean longer alignments factor in more heavily of all
+// the fragments of a query vs the reference that it mapped to
+//
+// this uses a combined key query+'-'+ref to iteratively map all the alignments
+// that match a particular ref from a particular query (so 1d array of what
+// could be a 2d map)
+//
+// the result is a single number that says e.g. chr5 from human mapped to chr5
+// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
+// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
+// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
+// this can show strong and weak levels of synteny, especially in polyploidy
+// situations
+function getWeightedMeans(ret) {
+    const scoreMap = {};
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const query = entry.qname;
+        const target = entry.tname;
+        const key = query + '-' + target;
+        if (!scoreMap[key]) {
+            scoreMap[key] = { quals: [], len: [] };
+        }
+        scoreMap[key].quals.push(entry.extra.mappingQual);
+        scoreMap[key].len.push(entry.extra.blockLen || 1);
+    }
+    const meanScoreMap = Object.fromEntries(Object.entries(scoreMap).map(([key, val]) => {
+        const vals = (0, util_1.zip)(val.quals, val.len);
+        return [key, weightedMean(vals)];
+    }));
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const query = entry.qname;
+        const target = entry.tname;
+        const key = query + '-' + target;
+        entry.extra.meanScore = meanScoreMap[key];
+    }
+    let min = 10000;
+    let max = 0;
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        min = Math.min(entry.extra.meanScore || 0, min);
+        max = Math.max(entry.extra.meanScore || 0, max);
+    }
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const b = entry.extra.meanScore || 0;
+        entry.extra.meanScore = (b - min) / (max - min);
+    }
+    return ret;
+}
+exports.getWeightedMeans = getWeightedMeans;
+// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
+function weightedMean(tuples) {
+    // eslint-disable-next-line unicorn/no-array-reduce
+    const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
+        valueSum + value * weight,
+        weightSum + weight,
+    ], [0, 0]);
+    return valueSum / weightSum;
+}
+function parsePAFLine(line) {
+    const [qname, , qstart, qend, strand, tname, , tstart, tend, numMatches, blockLen, mappingQual, ...fields] = line.split('\t');
+    const rest = Object.fromEntries(fields.map(field => {
+        const r = field.indexOf(':');
+        const fieldName = field.slice(0, r);
+        const fieldValue = field.slice(r + 3);
+        return [fieldName, fieldValue];
+    }));
+    return {
+        tname,
+        tstart: +tstart,
+        tend: +tend,
+        qname,
+        qstart: +qstart,
+        qend: +qend,
+        strand: strand === '-' ? -1 : 1,
+        extra: {
+            numMatches: +numMatches,
+            blockLen: +blockLen,
+            mappingQual: +mappingQual,
+            ...rest,
+        },
+    };
+}
+exports.parsePAFLine = parsePAFLine;
+function flipCigar(cigar) {
+    const arr = [];
+    for (let i = cigar.length - 2; i >= 0; i -= 2) {
+        arr.push(cigar[i]);
+        const op = cigar[i + 1];
+        if (op === 'D') {
+            arr.push('I');
+        }
+        else if (op === 'I') {
+            arr.push('D');
+        }
+        else {
+            arr.push(op);
+        }
+    }
+    return arr;
+}
+exports.flipCigar = flipCigar;
+function swapIndelCigar(cigar) {
+    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
+}
+exports.swapIndelCigar = swapIndelCigar;
+//# sourceMappingURL=util.js.map

package/dist/PAFAdapter/util.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class ComparativeAdaptersPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,51 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const PAFAdapter_1 = __importDefault(require("./PAFAdapter"));
+const MCScanAnchorsAdapter_1 = __importDefault(require("./MCScanAnchorsAdapter"));
+const MCScanSimpleAnchorsAdapter_1 = __importDefault(require("./MCScanSimpleAnchorsAdapter"));
+const MashMapAdapter_1 = __importDefault(require("./MashMapAdapter"));
+const DeltaAdapter_1 = __importDefault(require("./DeltaAdapter"));
+const ChainAdapter_1 = __importDefault(require("./ChainAdapter"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+class ComparativeAdaptersPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'ComparativeAdaptersPlugin';
+    }
+    install(pluginManager) {
+        (0, PAFAdapter_1.default)(pluginManager);
+        (0, DeltaAdapter_1.default)(pluginManager);
+        (0, ChainAdapter_1.default)(pluginManager);
+        (0, MCScanAnchorsAdapter_1.default)(pluginManager);
+        (0, MCScanSimpleAnchorsAdapter_1.default)(pluginManager);
+        (0, MashMapAdapter_1.default)(pluginManager);
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.paf/i;
+                const adapterName = 'PAFAdapter';
+                const fileName = (0, tracks_1.getFileName)(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        pafLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'PAFAdapter') {
+                    return 'SyntenyTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+    }
+}
+exports.default = ComparativeAdaptersPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/util.d.ts

@@ -0,0 +1,16 @@
+/// <reference types="node" />
+import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { GenericFilehandle } from 'generic-filehandle';
+import { PAFRecord } from './PAFAdapter/util';
+export declare function isGzip(buf: Buffer): boolean;
+export declare function parseBed(text: string): Map<string, {
+    refName: string;
+    start: number;
+    end: number;
+    score: number;
+    name: string;
+    strand: number;
+}>;
+export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
+export declare function zip(a: number[], b: number[]): [number, number][];
+export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];

package/dist/util.js

@@ -0,0 +1,57 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseLineByLine = exports.zip = exports.readFile = exports.parseBed = exports.isGzip = void 0;
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+exports.isGzip = isGzip;
+function parseBed(text) {
+    return new Map(text
+        .split(/\n|\r\n|\r/)
+        .filter(f => !!f || f.startsWith('#'))
+        .map(line => {
+        const [refName, start, end, name, score, strand] = line.split('\t');
+        return [
+            name,
+            {
+                refName,
+                start: +start,
+                end: +end,
+                score: +score,
+                name,
+                strand: strand === '-' ? -1 : 1,
+            },
+        ];
+    }));
+}
+exports.parseBed = parseBed;
+async function readFile(file, opts) {
+    const buffer = (await file.readFile(opts));
+    return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer);
+}
+exports.readFile = readFile;
+function zip(a, b) {
+    return a.map((e, i) => [e, b[i]]);
+}
+exports.zip = zip;
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+function parseLineByLine(buffer, cb) {
+    let blockStart = 0;
+    const entries = [];
+    while (blockStart < buffer.length) {
+        const n = buffer.indexOf('\n', blockStart);
+        if (n === -1) {
+            break;
+        }
+        const b = buffer.slice(blockStart, n);
+        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        if (line) {
+            entries.push(cb(line));
+        }
+        blockStart = n + 1;
+    }
+    return entries;
+}
+exports.parseLineByLine = parseLineByLine;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/ChainAdapter/ChainAdapter.d.ts

@@ -0,0 +1,19 @@
+import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+export default class ChainAdapter extends PAFAdapter {
+    setupPre(opts?: BaseOptions): Promise<{
+        qname: string;
+        qstart: number;
+        qend: number;
+        tname: string;
+        tstart: number;
+        tend: number;
+        strand: number;
+        extra: {
+            numMatches: number;
+            blockLen: number;
+            mappingQual: number;
+            cg: string;
+        };
+    }[]>;
+}

package/esm/ChainAdapter/ChainAdapter.js

@@ -0,0 +1,16 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { unzip } from '@gmod/bgzf-filehandle';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { paf_chain2paf } from './util';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class ChainAdapter extends PAFAdapter {
+    async setupPre(opts) {
+        const loc = openLocation(this.getConf('chainLocation'), this.pluginManager);
+        const buffer = (await loc.readFile(opts));
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        return paf_chain2paf(buf);
+    }
+}
+//# sourceMappingURL=ChainAdapter.js.map

package/esm/ChainAdapter/ChainAdapter.js.map

@@ -0,0 +1 @@
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package/esm/ChainAdapter/configSchema.d.ts

@@ -0,0 +1,39 @@
+declare const ChainAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     * can be specified as alternative to assemblyNames
+     */
+    targetAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     * can be specified as alternative to assemblyNames
+     */
+    queryAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    chainLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default ChainAdapter;

package/esm/ChainAdapter/configSchema.js

@@ -0,0 +1,43 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config ChainAdapter
+ * #category adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const ChainAdapter = ConfigurationSchema('ChainAdapter', {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Target is the first value in the array, query is the second',
+    },
+    /**
+     * #slot
+     * can be specified as alternative to assemblyNames
+     */
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the target assembly',
+    },
+    /**
+     * #slot
+     * can be specified as alternative to assemblyNames
+     */
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the query assembly',
+    },
+    /**
+     * #slot
+     */
+    chainLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+export default ChainAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/ChainAdapter/configSchema.js.map

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package/esm/ChainAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/ChainAdapter/index.js

@@ -0,0 +1,14 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'ChainAdapter',
+        displayName: 'Liftover chain adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./ChainAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/ChainAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/ChainAdapter/util.d.ts

@@ -0,0 +1,16 @@
+/// <reference types="node" />
+export declare function paf_chain2paf(buffer: Buffer): {
+    qname: string;
+    qstart: number;
+    qend: number;
+    tname: string;
+    tstart: number;
+    tend: number;
+    strand: number;
+    extra: {
+        numMatches: number;
+        blockLen: number;
+        mappingQual: number;
+        cg: string;
+    };
+}[];