@jbrowse/plugin-comparative-adapters 3.7.0 → 4.0.0

package/dist/PAFAdapter/configSchema.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const PAFAdapter = (0, configuration_1.ConfigurationSchema)('PAFAdapter', {
-    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: the target assembly name',
-    },
-    queryAssembly: {
-        type: 'string',
-        defaultValue: '',
-        description: 'Alternative to assemblyNames: the query assembly name',
-    },
-    pafLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/file.paf',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                pafLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = PAFAdapter;

package/dist/PAFAdapter/index.d.ts

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

package/dist/PAFAdapter/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 = PAFAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function PAFAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'PAFAdapter',
-        displayName: 'PAF adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            category: 'Synteny adapters',
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PAFAdapter'))).then(r => r.default),
-    }));
-}

package/dist/PAFAdapter/util.d.ts

@@ -1,17 +0,0 @@
-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[];

package/dist/PAFAdapter/util.js

@@ -1,45 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getWeightedMeans = getWeightedMeans;
-const util_1 = require("../util");
-function getWeightedMeans(ret) {
-    const scoreMap = {};
-    for (const entry of ret) {
-        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 || 1);
-        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 (const entry of ret) {
-        const query = entry.qname;
-        const target = entry.tname;
-        const key = `${query}-${target}`;
-        entry.extra.meanScore = meanScoreMap[key];
-    }
-    let min = 10000;
-    let max = 0;
-    for (const entry of ret) {
-        min = Math.min(entry.extra.meanScore || 0, min);
-        max = Math.max(entry.extra.meanScore || 0, max);
-    }
-    for (const entry of ret) {
-        const b = entry.extra.meanScore || 0;
-        entry.extra.meanScore = (b - min) / (max - min);
-    }
-    return ret;
-}
-function weightedMean(tuples) {
-    const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
-        valueSum + value * weight,
-        weightSum + weight,
-    ], [0, 0]);
-    return valueSum / weightSum;
-}

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -1,24 +0,0 @@
-import { TabixIndexedFile } from '@gmod/tabix';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-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 {
-    static capabilities: string[];
-    protected pif: TabixIndexedFile;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getAssemblyNames(): string[];
-    hasDataForRefName(): Promise<boolean>;
-    getRefNames(opts?: BaseOptions & {
-        regions?: Region[];
-    }): Promise<string[]>;
-    getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-}
-export {};

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -1,109 +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 tabix_1 = require("@gmod/tabix");
-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 SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
-const util_2 = require("../util");
-class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const pifGzLoc = this.getConf('pifGzLocation');
-        const type = this.getConf(['index', 'indexType']);
-        const loc = this.getConf(['index', 'location']);
-        const pm = this.pluginManager;
-        this.pif = new tabix_1.TabixIndexedFile({
-            filehandle: (0, io_1.openLocation)(pifGzLoc, pm),
-            csiFilehandle: type === 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
-            tbiFilehandle: type !== 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-        });
-    }
-    async getHeader(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading header', statusCallback, () => this.pif.getHeader());
-    }
-    getAssemblyNames() {
-        const assemblyNames = this.getConf('assemblyNames');
-        return assemblyNames.length === 0
-            ? [
-                this.getConf('queryAssembly'),
-                this.getConf('targetAssembly'),
-            ]
-            : assemblyNames;
-    }
-    async hasDataForRefName() {
-        return true;
-    }
-    async getRefNames(opts = {}) {
-        var _a, _b;
-        const r1 = (_b = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.assemblyName;
-        if (!r1) {
-            throw new Error('no assembly name provided');
-        }
-        const idx = this.getAssemblyNames().indexOf(r1);
-        const names = await this.pif.getReferenceSequenceNames(opts);
-        if (idx === 0) {
-            return names.filter(n => n.startsWith('q')).map(n => n.slice(1));
-        }
-        else if (idx === 1) {
-            return names.filter(n => n.startsWith('t')).map(n => n.slice(1));
-        }
-        else {
-            return [];
-        }
-    }
-    getFeatures(query, opts = {}) {
-        const { statusCallback = () => { } } = opts;
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { assemblyName } = query;
-            const assemblyNames = this.getAssemblyNames();
-            const index = assemblyNames.indexOf(assemblyName);
-            const flip = index === 0;
-            const letter = flip ? 'q' : 't';
-            await (0, util_1.updateStatus)('Downloading features', statusCallback, () => this.pif.getLines(letter + query.refName, query.start, query.end, {
-                lineCallback: (line, fileOffset) => {
-                    const r = (0, util_2.parsePAFLine)(line);
-                    const refName = r.qname.slice(1);
-                    const start = r.qstart;
-                    const end = r.qend;
-                    const mateName = r.tname;
-                    const mateStart = r.tstart;
-                    const mateEnd = r.tend;
-                    const { extra, strand } = r;
-                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
-                    observer.next(new SyntenyFeature_1.default({
-                        uniqueId: fileOffset + assemblyName,
-                        assemblyName,
-                        start,
-                        end,
-                        type: 'match',
-                        refName,
-                        strand,
-                        ...rest,
-                        CIGAR: extra.cg,
-                        syntenyId: fileOffset,
-                        identity: numMatches / blockLen,
-                        numMatches,
-                        blockLen,
-                        mate: {
-                            start: mateStart,
-                            end: mateEnd,
-                            refName: mateName,
-                            assemblyName: assemblyNames[+flip],
-                        },
-                    }));
-                },
-                stopToken: opts.stopToken,
-            }));
-            observer.complete();
-        });
-    }
-}
-PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = PAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -1,40 +0,0 @@
-declare const PairwiseIndexedPAFAdapter: 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;
-    };
-    pifGzLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
-            type: string;
-            defaultValue: string;
-        };
-        location: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default PairwiseIndexedPAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/configSchema.js

@@ -1,64 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const PairwiseIndexedPAFAdapter = (0, configuration_1.ConfigurationSchema)('PairwiseIndexedPAFAdapter', {
-    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: the target assembly name',
-    },
-    queryAssembly: {
-        type: 'string',
-        defaultValue: '',
-        description: 'Alternative to assemblyNames: the query assembly name',
-    },
-    pifGzLocation: {
-        type: 'fileLocation',
-        description: 'location of pairwise tabix indexed PAF (pif)',
-        defaultValue: {
-            uri: '/path/to/data/file.pif.gz',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'TBI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.paf.gz.tbi',
-                locationType: 'UriLocation',
-            },
-        },
-    }),
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                pifGzLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.tbi`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = PairwiseIndexedPAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/index.d.ts

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

package/dist/PairwiseIndexedPAFAdapter/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 = PairwiseIndexedPAFAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function PairwiseIndexedPAFAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'PairwiseIndexedPAFAdapter',
-        displayName: 'Pairwise indexed PAF adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            category: 'Synteny adapters',
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PairwiseIndexedPAFAdapter'))).then(r => r.default),
-    }));
-}

package/dist/SyntenyFeature/index.d.ts

@@ -1,4 +0,0 @@
-import { SimpleFeature } from '@jbrowse/core/util';
-export default class SyntenyFeature extends SimpleFeature {
-    get(arg: string): any;
-}

package/dist/SyntenyFeature/index.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("@jbrowse/core/util");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const { getMismatches } = plugin_alignments_1.MismatchParser;
-class SyntenyFeature extends util_1.SimpleFeature {
-    get(arg) {
-        if (arg === 'mismatches') {
-            return getMismatches(this.get('CIGAR'));
-        }
-        return super.get(arg);
-    }
-}
-exports.default = SyntenyFeature;

package/dist/index.d.ts

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

package/dist/index.js

@@ -1,37 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BlastTabularAdapter_1 = __importDefault(require("./BlastTabularAdapter"));
-const ChainAdapter_1 = __importDefault(require("./ChainAdapter"));
-const ComparativeAddTrackComponent_1 = __importDefault(require("./ComparativeAddTrackComponent"));
-const DeltaAdapter_1 = __importDefault(require("./DeltaAdapter"));
-const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
-const MCScanAddTrackComponent_1 = __importDefault(require("./MCScanAddTrackComponent"));
-const MCScanAnchorsAdapter_1 = __importDefault(require("./MCScanAnchorsAdapter"));
-const MCScanSimpleAnchorsAdapter_1 = __importDefault(require("./MCScanSimpleAnchorsAdapter"));
-const MashMapAdapter_1 = __importDefault(require("./MashMapAdapter"));
-const PAFAdapter_1 = __importDefault(require("./PAFAdapter"));
-const PairwiseIndexedPAFAdapter_1 = __importDefault(require("./PairwiseIndexedPAFAdapter"));
-class ComparativeAdaptersPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'ComparativeAdaptersPlugin';
-    }
-    install(pluginManager) {
-        (0, PAFAdapter_1.default)(pluginManager);
-        (0, PairwiseIndexedPAFAdapter_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);
-        (0, BlastTabularAdapter_1.default)(pluginManager);
-        (0, ComparativeAddTrackComponent_1.default)(pluginManager);
-        (0, MCScanAddTrackComponent_1.default)(pluginManager);
-        (0, GuessAdapter_1.default)(pluginManager);
-    }
-}
-exports.default = ComparativeAdaptersPlugin;

package/dist/syntenyTypes.d.ts

@@ -1,3 +0,0 @@
-export declare const syntenyTypes: string[];
-export declare const pairwiseTypes: string[];
-export declare const mcscanTypes: string[];

package/dist/syntenyTypes.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.mcscanTypes = exports.pairwiseTypes = exports.syntenyTypes = void 0;
-exports.syntenyTypes = [
-    'PAFAdapter',
-    'ChainAdapter',
-    'DeltaAdapter',
-    'BlastTabularAdapter',
-    'MashMapAdapter',
-    'MCScanAnchorsAdapter',
-    'MCScanSimpleAnchorsAdapter',
-    'PairwiseIndexedPAFAdapter',
-];
-exports.pairwiseTypes = [
-    'PAFAdapter',
-    'ChainAdapter',
-    'DeltaAdapter',
-    'MashMapAdapter',
-    'BlastTabularAdapter',
-    'PairwiseIndexedPAFAdapter',
-];
-exports.mcscanTypes = [
-    'MCScanAnchorsAdapter',
-    'MCScanSimpleAnchorsAdapter',
-];

package/dist/util.d.ts

@@ -1,16 +0,0 @@
-import type { PAFRecord } from './PAFAdapter/util';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { GenericFilehandle } from 'generic-filehandle2';
-export declare function parseBed(text: string): Map<string | undefined, {
-    refName: string | undefined;
-    start: number;
-    end: number;
-    score: number;
-    name: string | undefined;
-    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 parsePAFLine(line: string): PAFRecord;
-export declare function flipCigar(cigar: string[]): (string | undefined)[];
-export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -1,79 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseBed = parseBed;
-exports.readFile = readFile;
-exports.zip = zip;
-exports.parsePAFLine = parsePAFLine;
-exports.flipCigar = flipCigar;
-exports.swapIndelCigar = swapIndelCigar;
-const util_1 = require("@jbrowse/core/util");
-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,
-            },
-        ];
-    }));
-}
-async function readFile(file, opts) {
-    return (0, util_1.fetchAndMaybeUnzipText)(file, opts);
-}
-function zip(a, b) {
-    return a.map((e, i) => [e, b[i]]);
-}
-function parsePAFLine(line) {
-    const parts = line.split('\t');
-    const extraFields = parts.slice(12);
-    const extra = {
-        numMatches: +parts[9],
-        blockLen: +parts[10],
-        mappingQual: +parts[11],
-    };
-    if (extraFields.length) {
-        for (const field of extraFields) {
-            const colonIndex = field.indexOf(':');
-            extra[field.slice(0, colonIndex)] = field.slice(colonIndex + 3);
-        }
-    }
-    return {
-        tname: parts[5],
-        tstart: +parts[7],
-        tend: +parts[8],
-        qname: parts[0],
-        qstart: +parts[2],
-        qend: +parts[3],
-        strand: parts[4] === '-' ? -1 : 1,
-        extra,
-    };
-}
-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;
-}
-function swapIndelCigar(cigar) {
-    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
-}