@jbrowse/plugin-comparative-adapters 3.7.0 → 4.0.0

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -1,132 +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 util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const util_2 = require("../util");
-class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async setup(opts) {
-        if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts;
-        const assemblyNames = this.getConf('assemblyNames');
-        const pm = this.pluginManager;
-        const bed1 = (0, io_1.openLocation)(this.getConf('bed1Location'), pm);
-        const bed2 = (0, io_1.openLocation)(this.getConf('bed2Location'), pm);
-        const mcscan = (0, io_1.openLocation)(this.getConf('mcscanSimpleAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await (0, util_1.updateStatus)('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts))));
-        const bed1Map = (0, util_2.parseBed)(bed1text);
-        const bed2Map = (0, util_2.parseBed)(bed2text);
-        const feats = mcscantext
-            .split(/\n|\r\n|\r/)
-            .filter(f => !!f && f !== '###')
-            .map((line, index) => {
-            const [n11, n12, n21, n22, score, strand] = line.split('\t');
-            const r11 = bed1Map.get(n11);
-            const r12 = bed1Map.get(n12);
-            const r21 = bed2Map.get(n21);
-            const r22 = bed2Map.get(n22);
-            if (!r11 || !r12 || !r21 || !r22) {
-                throw new Error(`feature not found, ${n11} ${n12} ${n21} ${n22} ${r11} ${r12} ${r21} ${r22}`);
-            }
-            return [
-                r11,
-                r12,
-                r21,
-                r22,
-                +score,
-                strand === '-' ? -1 : 1,
-                index,
-            ];
-        });
-        return {
-            assemblyNames,
-            feats,
-        };
-    }
-    async hasDataForRefName() {
-        return true;
-    }
-    getAssemblyNames() {
-        const assemblyNames = this.getConf('assemblyNames');
-        return assemblyNames;
-    }
-    async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
-        const { feats } = await this.setup(opts);
-        const idx = this.getAssemblyNames().indexOf(r1);
-        if (idx !== -1) {
-            const set = new Set();
-            for (const feat of feats) {
-                if (idx === 0) {
-                    set.add(feat[0].refName);
-                    set.add(feat[1].refName);
-                }
-                else {
-                    set.add(feat[2].refName);
-                    set.add(feat[3].refName);
-                }
-            }
-            return [...set];
-        }
-        console.warn('Unable to do ref renaming on adapter');
-        return [];
-    }
-    getFeatures(region, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { assemblyNames, feats } = await this.setup(opts);
-            const index = assemblyNames.indexOf(region.assemblyName);
-            if (index !== -1) {
-                const flip = index === 0;
-                for (const f of feats) {
-                    const [f11, f12, f21, f22, score, strand, rowNum] = f;
-                    let r1 = {
-                        refName: f11.refName,
-                        start: Math.min(f11.start, f12.start),
-                        end: Math.max(f11.end, f12.end),
-                    };
-                    let r2 = {
-                        refName: f21.refName,
-                        start: Math.min(f21.start, f22.start),
-                        end: Math.max(f21.end, f22.end),
-                    };
-                    if (!flip) {
-                        ;
-                        [r2, r1] = [r1, r2];
-                    }
-                    if (r1.refName === region.refName &&
-                        (0, util_1.doesIntersect2)(r1.start, r1.end, region.start, region.end)) {
-                        observer.next(new simpleFeature_1.default({
-                            ...r1,
-                            uniqueId: `${rowNum}`,
-                            syntenyId: rowNum,
-                            assemblyName: assemblyNames[+!flip],
-                            score,
-                            strand,
-                            mate: {
-                                ...r2,
-                                assemblyName: assemblyNames[+flip],
-                            },
-                        }));
-                    }
-                }
-            }
-            observer.complete();
-        });
-    }
-}
-MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = MCScanAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/configSchema.d.ts

@@ -1,28 +0,0 @@
-declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    mcscanSimpleAnchorsLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    bed1Location: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    bed2Location: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default MCScanSimpleAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanSimpleAnchorsAdapter', {
-    mcscanSimpleAnchorsLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/mcscan.anchors.simple',
-            locationType: 'UriLocation',
-        },
-    },
-    bed1Location: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/file.bed',
-            locationType: 'UriLocation',
-        },
-    },
-    bed2Location: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/file.bed',
-            locationType: 'UriLocation',
-        },
-    },
-    assemblyNames: {
-        type: 'stringArray',
-        defaultValue: [],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri && snap.bed1 && snap.bed2
-            ? {
-                ...snap,
-                mcscanSimpleAnchorsLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                bed1Location: {
-                    uri: snap.bed1,
-                    baseUri: snap.baseUri,
-                },
-                bed2Location: {
-                    uri: snap.bed2,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = MCScanSimpleAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/index.d.ts

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

package/dist/MCScanSimpleAnchorsAdapter/index.js

@@ -1,52 +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 = MCScanSimpleAnchorsAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function MCScanSimpleAnchorsAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'MCScanSimpleAnchorsAdapter',
-        displayName: 'MCScan anchors.simple adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            category: 'Synteny adapters',
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanSimpleAnchorsAdapter'))).then(r => r.default),
-    }));
-}

package/dist/MashMapAdapter/MashMapAdapter.d.ts

@@ -1,16 +0,0 @@
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class MashMapAdapter extends PAFAdapter {
-    setupPre(opts?: BaseOptions): Promise<{
-        tname: string;
-        tstart: number;
-        tend: number;
-        qname: string;
-        qstart: number;
-        qend: number;
-        strand: number;
-        extra: {
-            mappingQual: number;
-        };
-    }[]>;
-}

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -1,39 +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 util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
-class MashMapAdapter extends PAFAdapter_1.default {
-    async setupPre(opts) {
-        const lines = [];
-        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager), opts), line => {
-            lines.push(parseMashMapLine(line));
-            return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        return lines;
-    }
-}
-exports.default = MashMapAdapter;
-function parseMashMapLine(line) {
-    const fields = line.split(' ');
-    if (fields.length < 9) {
-        throw new Error(`improperly formatted line: ${line}`);
-    }
-    const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;
-    return {
-        tname: tname,
-        tstart: +tstart,
-        tend: +tend,
-        qname: qname,
-        qstart: +qstart,
-        qend: +qend,
-        strand: strand === '-' ? -1 : 1,
-        extra: {
-            mappingQual: +mq,
-        },
-    };
-}

package/dist/MashMapAdapter/configSchema.d.ts

@@ -1,25 +0,0 @@
-declare const MashMapAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    targetAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    queryAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    outLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default MashMapAdapter;

package/dist/MashMapAdapter/configSchema.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const MashMapAdapter = (0, configuration_1.ConfigurationSchema)('MashMapAdapter', {
-    assemblyNames: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
-    },
-    targetAssembly: {
-        type: 'string',
-        defaultValue: '',
-        description: 'Alternative to assemblyNames array: the target assembly',
-    },
-    queryAssembly: {
-        type: 'string',
-        defaultValue: '',
-        description: 'Alternative to assemblyNames array: the query assembly',
-    },
-    outLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/mashmap.out',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                outLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = MashMapAdapter;

package/dist/MashMapAdapter/index.d.ts

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

package/dist/MashMapAdapter/index.js

@@ -1,52 +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 = MashMapAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function MashMapAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'MashMapAdapter',
-        displayName: 'MashMap adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            category: 'Synteny adapters',
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MashMapAdapter'))).then(r => r.default),
-    }));
-}

package/dist/PAFAdapter/PAFAdapter.d.ts

@@ -1,20 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { PAFRecord } from './util';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util';
-import type { Region } from '@jbrowse/core/util/types';
-interface PAFOptions extends BaseOptions {
-    config?: AnyConfigurationModel;
-}
-export default class PAFAdapter extends BaseFeatureDataAdapter {
-    private setupP?;
-    static capabilities: string[];
-    setup(opts?: BaseOptions): Promise<PAFRecord[]>;
-    setupPre(opts?: BaseOptions): Promise<PAFRecord[]>;
-    hasDataForRefName(): Promise<boolean>;
-    getAssemblyNames(): string[];
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-}
-export {};

package/dist/PAFAdapter/PAFAdapter.js

@@ -1,137 +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 util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const range_1 = require("@jbrowse/core/util/range");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
-const util_2 = require("../util");
-const util_3 = require("./util");
-const { parseCigar } = plugin_alignments_1.MismatchParser;
-class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async setup(opts) {
-        if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async setupPre(opts) {
-        const lines = [];
-        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('pafLocation'), this.pluginManager), opts), line => {
-            lines.push((0, util_2.parsePAFLine)(line));
-            return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        return lines;
-    }
-    async hasDataForRefName() {
-        return true;
-    }
-    getAssemblyNames() {
-        const assemblyNames = this.getConf('assemblyNames');
-        if (assemblyNames.length === 0) {
-            const query = this.getConf('queryAssembly');
-            const target = this.getConf('targetAssembly');
-            return [query, target];
-        }
-        return assemblyNames;
-    }
-    async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
-        const feats = await this.setup(opts);
-        const idx = this.getAssemblyNames().indexOf(r1);
-        if (idx !== -1) {
-            const set = new Set();
-            for (const feat of feats) {
-                set.add(idx === 0 ? feat.qname : feat.tname);
-            }
-            return [...set];
-        }
-        console.warn('Unable to do ref renaming on adapter');
-        return [];
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const pafRecords = (0, util_3.getWeightedMeans)(await this.setup(opts));
-            const assemblyNames = this.getAssemblyNames();
-            const { start: qstart, end: qend, refName: qref, assemblyName } = query;
-            const index = assemblyNames.indexOf(assemblyName);
-            const flip = index === 0;
-            if (index === -1) {
-                console.warn(`${assemblyName} not found in this adapter`);
-                observer.complete();
-            }
-            for (let i = 0; i < pafRecords.length; i++) {
-                const r = pafRecords[i];
-                let start = 0;
-                let end = 0;
-                let refName = '';
-                let mateName = '';
-                let mateStart = 0;
-                let mateEnd = 0;
-                if (flip) {
-                    start = r.qstart;
-                    end = r.qend;
-                    refName = r.qname;
-                    mateName = r.tname;
-                    mateStart = r.tstart;
-                    mateEnd = r.tend;
-                }
-                else {
-                    start = r.tstart;
-                    end = r.tend;
-                    refName = r.tname;
-                    mateName = r.qname;
-                    mateStart = r.qstart;
-                    mateEnd = r.qend;
-                }
-                const { extra, strand } = r;
-                if (refName === qref && (0, range_1.doesIntersect2)(qstart, qend, start, end)) {
-                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
-                    let CIGAR = extra.cg;
-                    if (extra.cg) {
-                        if (flip && strand === -1) {
-                            CIGAR = (0, util_2.flipCigar)(parseCigar(extra.cg)).join('');
-                        }
-                        else if (flip) {
-                            CIGAR = (0, util_2.swapIndelCigar)(extra.cg);
-                        }
-                    }
-                    observer.next(new SyntenyFeature_1.default({
-                        uniqueId: i + assemblyName,
-                        assemblyName,
-                        start,
-                        end,
-                        type: 'match',
-                        refName,
-                        strand,
-                        ...rest,
-                        CIGAR,
-                        syntenyId: i,
-                        identity: numMatches / blockLen,
-                        numMatches,
-                        blockLen,
-                        mate: {
-                            start: mateStart,
-                            end: mateEnd,
-                            refName: mateName,
-                            assemblyName: assemblyNames[+flip],
-                        },
-                    }));
-                }
-            }
-            observer.complete();
-        });
-    }
-}
-PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = PAFAdapter;

package/dist/PAFAdapter/configSchema.d.ts

@@ -1,25 +0,0 @@
-declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    targetAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    queryAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    pafLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default PAFAdapter;