@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/CramAdapter/CramAdapter.js

@@ -1,228 +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 cram_1 = require("@gmod/cram");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const rxjs_2 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
-const util_2 = require("../shared/util");
-class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.samHeader = {};
-        this.ultraLongFeatureCache = new QuickLRU_1.default({
-            maxSize: 500,
-        });
-        this.seqIdToOriginalRefName = [];
-    }
-    async configurePre() {
-        const cramLocation = this.getConf('cramLocation');
-        const craiLocation = this.getConf('craiLocation');
-        const pm = this.pluginManager;
-        const cram = new cram_1.IndexedCramFile({
-            cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
-            index: new cram_1.CraiIndex({
-                filehandle: (0, io_1.openLocation)(craiLocation, pm),
-            }),
-            seqFetch: (...args) => this.seqFetch(...args),
-            checkSequenceMD5: false,
-        });
-        if (!this.getSubAdapter) {
-            throw new Error('Error getting subadapter');
-        }
-        const seqConf = this.getConf('sequenceAdapter');
-        if (!seqConf) {
-            throw new Error('no sequenceAdapter supplied to CramAdapter config');
-        }
-        const subadapter = await this.getSubAdapter(seqConf);
-        return {
-            cram,
-            sequenceAdapter: subadapter.dataAdapter,
-        };
-    }
-    async configure() {
-        if (!this.configureP) {
-            this.configureP = this.configurePre().catch((e) => {
-                this.configureP = undefined;
-                throw e;
-            });
-        }
-        return this.configureP;
-    }
-    async getHeader(_opts) {
-        const { cram } = await this.configure();
-        return cram.cram.getHeaderText();
-    }
-    async seqFetch(seqId, start, end) {
-        start -= 1;
-        const { sequenceAdapter } = await this.configure();
-        const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
-        if (!refName) {
-            throw new Error('unknown');
-        }
-        const seqChunks = await (0, rxjs_2.firstValueFrom)(sequenceAdapter
-            .getFeatures({
-            refName,
-            start,
-            end,
-            assemblyName: '',
-        })
-            .pipe((0, operators_1.toArray)()));
-        const sequence = seqChunks
-            .sort((a, b) => a.get('start') - b.get('start'))
-            .map(chunk => {
-            const chunkStart = chunk.get('start');
-            const chunkEnd = chunk.get('end');
-            const trimStart = Math.max(start - chunkStart, 0);
-            const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
-            const trimLength = trimEnd - trimStart;
-            const chunkSeq = chunk.get('seq') || chunk.get('residues');
-            return chunkSeq.slice(trimStart, trimStart + trimLength);
-        })
-            .join('');
-        const qlen = end - start;
-        if (sequence.length !== qlen) {
-            throw new Error(`fetching ${refName}:${(0, util_1.toLocale)(start - 1)}-${(0, util_1.toLocale)(end)} returned ${(0, util_1.toLocale)(sequence.length)} bases, should have returned ${(0, util_1.toLocale)(qlen)}`);
-        }
-        return sequence;
-    }
-    async setupPre(_opts) {
-        const conf = await this.configure();
-        const { cram } = conf;
-        const samHeader = await cram.cram.getSamHeader();
-        const idToName = [];
-        const nameToId = {};
-        for (const [refId, sqLine] of samHeader
-            .filter(l => l.tag === 'SQ')
-            .entries()) {
-            const SN = sqLine.data.find(item => item.tag === 'SN');
-            if (SN) {
-                const refName = SN.value;
-                nameToId[refName] = refId;
-                idToName[refId] = refName;
-            }
-        }
-        const readGroups = samHeader
-            .filter(l => l.tag === 'RG')
-            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
-        const data = { idToName, nameToId, readGroups };
-        this.samHeader = data;
-        return {
-            samHeader: data,
-            ...conf,
-        };
-    }
-    async setupPre2(opts) {
-        if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async setup(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.setupPre2(opts));
-    }
-    async getRefNames(opts) {
-        const { samHeader } = await this.setup(opts);
-        if (!samHeader.idToName) {
-            throw new Error('CRAM file has no header lines');
-        }
-        return samHeader.idToName;
-    }
-    refNameToId(refName) {
-        if (this.samHeader.nameToId) {
-            return this.samHeader.nameToId[refName];
-        }
-        if (this.seqIdToRefName) {
-            return this.seqIdToRefName.indexOf(refName);
-        }
-        return undefined;
-    }
-    refIdToName(refId) {
-        var _a, _b;
-        return ((_a = this.samHeader.idToName) === null || _a === void 0 ? void 0 : _a[refId]) || ((_b = this.seqIdToRefName) === null || _b === void 0 ? void 0 : _b[refId]);
-    }
-    refIdToOriginalName(refId) {
-        return this.seqIdToOriginalRefName[refId];
-    }
-    getFeatures(region, opts) {
-        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
-        const { refName, start, end, originalRefName } = region;
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { cram, samHeader } = await this.setup(opts);
-            const refId = this.refNameToId(refName);
-            if (refId === undefined) {
-                console.warn('Unknown refName', refName);
-                observer.complete();
-                return;
-            }
-            if (originalRefName) {
-                this.seqIdToOriginalRefName[refId] = originalRefName;
-            }
-            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
-            (0, stopToken_1.checkStopToken)(stopToken);
-            await (0, util_1.updateStatus)('Processing alignments', statusCallback, () => {
-                var _a;
-                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-                for (const record of records) {
-                    if ((0, util_2.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
-                        continue;
-                    }
-                    if (tagFilter &&
-                        (0, util_2.filterTagValue)(tagFilter.tag === 'RG'
-                            ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
-                            : record.tags[tagFilter.tag], tagFilter.value)) {
-                        continue;
-                    }
-                    if (readName && record.readName !== readName) {
-                        continue;
-                    }
-                    const ret = this.ultraLongFeatureCache.get(`${record.uniqueId}`);
-                    if (!ret) {
-                        const elt = this.cramRecordToFeature(record);
-                        this.ultraLongFeatureCache.set(`${record.uniqueId}`, elt);
-                        observer.next(elt);
-                    }
-                    else {
-                        observer.next(ret);
-                    }
-                }
-                observer.complete();
-            });
-        }, stopToken);
-    }
-    cramRecordToFeature(record) {
-        return new CramSlightlyLazyFeature_1.default(record, this);
-    }
-    async getMultiRegionFeatureDensityStats(regions, opts) {
-        const bytes = await this.bytesForRegions(regions, opts);
-        const fetchSizeLimit = this.getConf('fetchSizeLimit');
-        return {
-            bytes,
-            fetchSizeLimit,
-        };
-    }
-    async bytesForRegions(regions, _opts) {
-        const { cram } = await this.configure();
-        const blockResults = await Promise.all(regions.map(region => {
-            const { refName, start, end } = region;
-            const chrId = this.refNameToId(refName);
-            return chrId !== undefined
-                ? cram.index.getEntriesForRange(chrId, start, end)
-                : [{ sliceBytes: 0 }];
-        }));
-        return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
-    }
-}
-exports.default = CramAdapter;

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,33 +0,0 @@
-import type CramAdapter from './CramAdapter';
-import type { CramRecord } from '@gmod/cram';
-import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default class CramSlightlyLazyFeature implements Feature {
-    private record;
-    private _store;
-    constructor(record: CramRecord, _store: CramAdapter);
-    get name(): string | undefined;
-    get start(): number;
-    get end(): number;
-    get score(): number | undefined;
-    get flags(): number;
-    get strand(): 1 | -1;
-    get qual(): string;
-    get qualRaw(): number[] | null | undefined;
-    get refName(): string;
-    get pair_orientation(): string | null | undefined;
-    get template_length(): number | undefined;
-    get next_ref(): string | undefined;
-    get next_segment_position(): string | undefined;
-    get is_paired(): boolean;
-    get next_pos(): number | undefined;
-    get tags(): Record<string, string>;
-    get seq(): string | null | undefined;
-    get CIGAR(): string;
-    id(): string;
-    get(field: string): any;
-    parent(): undefined;
-    children(): undefined;
-    get mismatches(): import("../shared/types").Mismatch[];
-    get fields(): SimpleFeatureSerialized;
-    toJSON(): SimpleFeatureSerialized;
-}

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,124 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("./util");
-const util_2 = require("../shared/util");
-class CramSlightlyLazyFeature {
-    constructor(record, _store) {
-        this.record = record;
-        this._store = _store;
-    }
-    get name() {
-        return this.record.readName;
-    }
-    get start() {
-        return this.record.alignmentStart - 1;
-    }
-    get end() {
-        var _a;
-        return this.start + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1);
-    }
-    get score() {
-        return this.record.mappingQuality;
-    }
-    get flags() {
-        return this.record.flags;
-    }
-    get strand() {
-        return this.record.isReverseComplemented() ? -1 : 1;
-    }
-    get qual() {
-        return (this.record.qualityScores || []).join(' ');
-    }
-    get qualRaw() {
-        return this.record.qualityScores;
-    }
-    get refName() {
-        return this._store.refIdToName(this.record.sequenceId);
-    }
-    get pair_orientation() {
-        return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    }
-    get template_length() {
-        return this.record.templateLength || this.record.templateSize;
-    }
-    get next_ref() {
-        return this.record.mate
-            ? this._store.refIdToName(this.record.mate.sequenceId)
-            : undefined;
-    }
-    get next_segment_position() {
-        return this.record.mate
-            ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
-            : undefined;
-    }
-    get is_paired() {
-        return !!this.record.mate;
-    }
-    get next_pos() {
-        var _a;
-        return (_a = this.record.mate) === null || _a === void 0 ? void 0 : _a.alignmentStart;
-    }
-    get tags() {
-        var _a;
-        const RG = (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
-        return RG !== undefined ? { ...this.record.tags, RG } : this.record.tags;
-    }
-    get seq() {
-        return this.record.getReadBases();
-    }
-    get CIGAR() {
-        return (0, util_1.readFeaturesToCIGAR)(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
-    }
-    id() {
-        return `${this._store.id}-${this.record.uniqueId}`;
-    }
-    get(field) {
-        return field === 'mismatches'
-            ? this.mismatches
-            : field === 'qual'
-                ? this.qual
-                : field === 'CIGAR'
-                    ? this.CIGAR
-                    : this.fields[field];
-    }
-    parent() {
-        return undefined;
-    }
-    children() {
-        return undefined;
-    }
-    get mismatches() {
-        return (0, util_1.readFeaturesToMismatches)(this.record.readFeatures, this.start, this.qualRaw);
-    }
-    get fields() {
-        return {
-            start: this.start,
-            name: this.name,
-            end: this.end,
-            score: this.score,
-            strand: this.strand,
-            template_length: this.template_length,
-            flags: this.flags,
-            tags: this.tags,
-            refName: this.refName,
-            seq: this.seq,
-            type: 'match',
-            pair_orientation: this.pair_orientation,
-            next_ref: this.next_ref,
-            next_pos: this.next_pos,
-            next_segment_position: this.next_segment_position,
-            uniqueId: this.id(),
-        };
-    }
-    toJSON() {
-        return {
-            ...this.fields,
-            CIGAR: this.CIGAR,
-            qual: this.qual,
-        };
-    }
-}
-exports.default = CramSlightlyLazyFeature;
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'fields');
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'CIGAR');
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'mismatches');

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -1,28 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { Observable } from 'rxjs';
-import type { GenericFilehandle } from 'generic-filehandle2';
-export declare function parseSmallFasta(text: string): {
-    id: string;
-    description: string;
-    sequence: string;
-}[];
-type FileHandle = GenericFilehandle;
-export declare class FetchableSmallFasta {
-    data: Promise<ReturnType<typeof parseSmallFasta>>;
-    constructor(filehandle: FileHandle);
-    fetch(id: number, start: number, end: number): Promise<string>;
-    getSequenceList(): Promise<string[]>;
-}
-export declare class SequenceAdapter extends BaseFeatureDataAdapter {
-    fasta: FetchableSmallFasta;
-    refNames: string[];
-    constructor(filehandle: FileHandle);
-    getRefNames(): Promise<string[]>;
-    getFeatures({ refName, start, end, }: {
-        refName: string;
-        start: number;
-        end: number;
-    }): Observable<SimpleFeature>;
-}
-export {};

package/dist/CramAdapter/CramTestAdapters.js

@@ -1,85 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SequenceAdapter = exports.FetchableSmallFasta = void 0;
-exports.parseSmallFasta = parseSmallFasta;
-const configuration_1 = require("@jbrowse/core/configuration");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const rxjs_1 = require("rxjs");
-function parseSmallFasta(text) {
-    return text
-        .split('>')
-        .filter(t => /\S/.test(t))
-        .map(entryText => {
-        const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
-        const [id, ...descriptionLines] = defLine.split(' ');
-        const description = descriptionLines.join(' ');
-        const sequence = seqLines.join('').replaceAll(/\s/g, '');
-        return {
-            id: id,
-            description,
-            sequence,
-        };
-    });
-}
-class FetchableSmallFasta {
-    constructor(filehandle) {
-        this.data = filehandle.readFile().then(buffer => {
-            const decoder = new TextDecoder('utf8');
-            const text = decoder.decode(buffer);
-            return parseSmallFasta(text);
-        });
-    }
-    async fetch(id, start, end) {
-        const data = await this.data;
-        const entry = data[id];
-        const length = end - start + 1;
-        if (!entry) {
-            throw new Error(`no sequence with id ${id} exists`);
-        }
-        return entry.sequence.slice(start, start + length);
-    }
-    async getSequenceList() {
-        const data = await this.data;
-        return data.map(entry => entry.id);
-    }
-}
-exports.FetchableSmallFasta = FetchableSmallFasta;
-class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor(filehandle) {
-        super((0, configuration_1.ConfigurationSchema)('empty', {}).create());
-        this.refNames = [];
-        this.fasta = new FetchableSmallFasta(filehandle);
-    }
-    async getRefNames() {
-        return this.refNames;
-    }
-    getFeatures({ refName, start, end, }) {
-        return new rxjs_1.Observable(observer => {
-            this.fasta
-                .getSequenceList()
-                .then(refNames => {
-                this.refNames = refNames;
-            })
-                .then(() => this.fasta.fetch(this.refNames.indexOf(refName), start, end))
-                .then(ret => {
-                observer.next(new simpleFeature_1.default({
-                    uniqueId: `${refName}-${start}-${end}`,
-                    refName,
-                    seq: ret,
-                    start,
-                    end,
-                }));
-                observer.complete();
-            })
-                .catch((e) => {
-                observer.error(e);
-            });
-            return { unsubscribe: () => { } };
-        });
-    }
-}
-exports.SequenceAdapter = SequenceAdapter;

package/dist/CramAdapter/configSchema.d.ts

@@ -1,27 +0,0 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    fetchSizeLimit: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    cramLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    craiLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default configSchema;

package/dist/CramAdapter/configSchema.js

@@ -1,48 +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)('CramAdapter', {
-    fetchSizeLimit: {
-        type: 'number',
-        description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
-        defaultValue: 3000000,
-    },
-    cramLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.cram',
-            locationType: 'UriLocation',
-        },
-    },
-    craiLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.cram.crai',
-            locationType: 'UriLocation',
-        },
-    },
-    sequenceAdapter: {
-        type: 'frozen',
-        description: 'sequence data adapter',
-        defaultValue: null,
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                cramLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                craiLocation: {
-                    uri: `${snap.uri}.crai`,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = configSchema;

package/dist/CramAdapter/index.d.ts

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

package/dist/CramAdapter/index.js

@@ -1,51 +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 = CramAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function CramAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'CramAdapter',
-            displayName: 'CRAM adapter',
-            configSchema: configSchema_1.default,
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/CramAdapter/util.d.ts

@@ -1,9 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
-    seq: string;
-    start: number;
-}): string;
-export {};