@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/AlignmentsTrack/index.js

@@ -1,23 +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.default = register;
-const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const configSchemaF_1 = __importDefault(require("./configSchemaF"));
-function register(pm) {
-    pm.addTrackType(() => {
-        const configSchema = (0, configSchemaF_1.default)(pm);
-        const track = new TrackType_1.default({
-            name: 'AlignmentsTrack',
-            displayName: 'Alignments track',
-            configSchema,
-            stateModel: (0, models_1.createBaseTrackModel)(pm, 'AlignmentsTrack', configSchema),
-        });
-        const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay');
-        track.addDisplayType(linearAlignmentsDisplay);
-        return track;
-    });
-}

package/dist/BamAdapter/BamAdapter.d.ts

@@ -1,44 +0,0 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { FilterBy } from '../shared/types';
-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 Header {
-    idToName: string[];
-    nameToId: Record<string, number>;
-}
-export default class BamAdapter extends BaseFeatureDataAdapter {
-    private samHeader?;
-    private setupP?;
-    private ultraLongFeatureCache;
-    private configureP?;
-    protected configurePre(): Promise<{
-        bam: BamFile;
-        sequenceAdapter: BaseFeatureDataAdapter;
-    } | {
-        bam: BamFile;
-        sequenceAdapter?: undefined;
-    }>;
-    protected configure(): Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter;
-    }>;
-    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
-    private setupPre;
-    setupPre2(opts?: BaseOptions): Promise<Header>;
-    setup(opts?: BaseOptions): Promise<Header>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    private seqFetch;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions & {
-        filterBy: FilterBy;
-    }): import("rxjs").Observable<Feature>;
-    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
-        bytes: number;
-        fetchSizeLimit: any;
-    }>;
-    refIdToName(refId: number): string | undefined;
-}
-export {};

package/dist/BamAdapter/BamAdapter.js

@@ -1,181 +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 bam_1 = require("@gmod/bam");
-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 BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
-const util_2 = require("../shared/util");
-class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.ultraLongFeatureCache = new QuickLRU_1.default({
-            maxSize: 500,
-        });
-    }
-    async configurePre() {
-        const bamLocation = this.getConf('bamLocation');
-        const location = this.getConf(['index', 'location']);
-        const indexType = this.getConf(['index', 'indexType']);
-        const pm = this.pluginManager;
-        const csi = indexType === 'CSI';
-        const bam = new bam_1.BamFile({
-            bamFilehandle: (0, io_1.openLocation)(bamLocation, pm),
-            csiFilehandle: csi ? (0, io_1.openLocation)(location, pm) : undefined,
-            baiFilehandle: !csi ? (0, io_1.openLocation)(location, pm) : undefined,
-            yieldThreadTime: Number.POSITIVE_INFINITY,
-        });
-        const adapterConfig = this.getConf('sequenceAdapter');
-        if (adapterConfig && this.getSubAdapter) {
-            const { dataAdapter } = await this.getSubAdapter(adapterConfig);
-            return {
-                bam,
-                sequenceAdapter: dataAdapter,
-            };
-        }
-        return { bam };
-    }
-    async configure() {
-        if (!this.configureP) {
-            this.configureP = this.configurePre().catch((e) => {
-                this.configureP = undefined;
-                throw e;
-            });
-        }
-        return this.configureP;
-    }
-    async getHeader(_opts) {
-        const { bam } = await this.configure();
-        return bam.getHeaderText();
-    }
-    async setupPre(_opts) {
-        const { bam } = await this.configure();
-        const samHeader = await bam.getHeader();
-        const idToName = [];
-        const nameToId = {};
-        if (samHeader) {
-            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;
-                }
-            }
-        }
-        this.samHeader = { idToName, nameToId };
-        return this.samHeader;
-    }
-    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 { idToName } = await this.setup(opts);
-        return idToName;
-    }
-    async seqFetch(refName, start, end) {
-        const { sequenceAdapter } = await this.configure();
-        const refSeqStore = sequenceAdapter;
-        if (!refSeqStore) {
-            return undefined;
-        }
-        if (!refName) {
-            return undefined;
-        }
-        const features = refSeqStore.getFeatures({
-            refName,
-            start,
-            end,
-            assemblyName: '',
-        });
-        const seqChunks = await (0, rxjs_2.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
-        let sequence = '';
-        for (const chunk of seqChunks.sort((a, b) => a.get('start') - b.get('start'))) {
-            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');
-            sequence += chunkSeq.slice(trimStart, trimStart + trimLength);
-        }
-        if (sequence.length !== end - start) {
-            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
-        }
-        return sequence;
-    }
-    getFeatures(region, opts) {
-        const { refName, start, end, originalRefName } = region;
-        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { bam } = await this.configure();
-            await this.setup(opts);
-            (0, stopToken_1.checkStopToken)(stopToken);
-            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end));
-            (0, stopToken_1.checkStopToken)(stopToken);
-            await (0, util_1.updateStatus)('Processing alignments', statusCallback, async () => {
-                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-                for (const record of records) {
-                    let ref;
-                    if (!record.tags.MD) {
-                        ref = await this.seqFetch(originalRefName || refName, record.start, record.end);
-                    }
-                    if ((0, util_2.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
-                        continue;
-                    }
-                    if (tagFilter &&
-                        (0, util_2.filterTagValue)(record.tags[tagFilter.tag], tagFilter.value)) {
-                        continue;
-                    }
-                    if (readName && record.name !== readName) {
-                        continue;
-                    }
-                    const ret = this.ultraLongFeatureCache.get(`${record.id}`);
-                    if (!ret) {
-                        const elt = new BamSlightlyLazyFeature_1.default(record, this, ref);
-                        this.ultraLongFeatureCache.set(`${record.id}`, elt);
-                        observer.next(elt);
-                    }
-                    else {
-                        observer.next(ret);
-                    }
-                }
-                observer.complete();
-            });
-        });
-    }
-    async getMultiRegionFeatureDensityStats(regions, opts) {
-        const { bam } = await this.configure();
-        if (bam.index) {
-            const bytes = await (0, util_1.bytesForRegions)(regions, bam);
-            const fetchSizeLimit = this.getConf('fetchSizeLimit');
-            return { bytes, fetchSizeLimit };
-        }
-        return super.getMultiRegionFeatureDensityStats(regions, opts);
-    }
-    refIdToName(refId) {
-        var _a;
-        return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];
-    }
-}
-exports.default = BamAdapter;

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,17 +0,0 @@
-import type BamAdapter from './BamAdapter';
-import type { BamRecord } from '@gmod/bam';
-import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-export default class BamSlightlyLazyFeature implements Feature {
-    private record;
-    private adapter;
-    private ref?;
-    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
-    id(): string;
-    get mismatches(): import("../shared/types").Mismatch[];
-    get qual(): string | undefined;
-    get(field: string): any;
-    parent(): undefined;
-    children(): undefined;
-    get fields(): SimpleFeatureSerialized;
-    toJSON(): SimpleFeatureSerialized;
-}

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,69 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const MismatchParser_1 = require("../MismatchParser");
-const util_1 = require("../shared/util");
-class BamSlightlyLazyFeature {
-    constructor(record, adapter, ref) {
-        this.record = record;
-        this.adapter = adapter;
-        this.ref = ref;
-    }
-    id() {
-        return `${this.adapter.id}-${this.record.id}`;
-    }
-    get mismatches() {
-        return (0, MismatchParser_1.getMismatches)(this.record.CIGAR, this.record.tags.MD, this.record.seq, this.ref, this.record.qual);
-    }
-    get qual() {
-        var _a;
-        return (_a = this.record.qual) === null || _a === void 0 ? void 0 : _a.join(' ');
-    }
-    get(field) {
-        return field === 'mismatches'
-            ? this.mismatches
-            : field === 'qual'
-                ? this.qual
-                : this.fields[field];
-    }
-    parent() {
-        return undefined;
-    }
-    children() {
-        return undefined;
-    }
-    get fields() {
-        const r = this.record;
-        const a = this.adapter;
-        const p = r.isPaired();
-        return {
-            start: r.start,
-            name: r.name,
-            end: r.end,
-            score: r.score,
-            strand: r.strand,
-            template_length: r.template_length,
-            flags: r.flags,
-            tags: r.tags,
-            refName: a.refIdToName(r.ref_id),
-            CIGAR: r.CIGAR,
-            seq: r.seq,
-            type: 'match',
-            pair_orientation: r.pair_orientation,
-            next_ref: p ? a.refIdToName(r.next_refid) : undefined,
-            next_pos: p ? r.next_pos : undefined,
-            next_segment_position: p
-                ? `${a.refIdToName(r.next_refid)}:${r.next_pos + 1}`
-                : undefined,
-            uniqueId: this.id(),
-        };
-    }
-    toJSON() {
-        return {
-            ...this.fields,
-            qual: this.qual,
-        };
-    }
-}
-exports.default = BamSlightlyLazyFeature;
-(0, util_1.cacheGetter)(BamSlightlyLazyFeature, 'fields');
-(0, util_1.cacheGetter)(BamSlightlyLazyFeature, 'mismatches');

package/dist/BamAdapter/configSchema.d.ts

@@ -1,34 +0,0 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bamLocation: {
-        type: 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>>;
-    fetchSizeLimit: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default configSchema;

package/dist/BamAdapter/configSchema.js

@@ -1,58 +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 configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
-    bamLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.bam',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('BamIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['BAI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'BAI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.bam.bai',
-                locationType: 'UriLocation',
-            },
-        },
-    }),
-    fetchSizeLimit: {
-        type: 'number',
-        description: 'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
-        defaultValue: 5000000,
-    },
-    sequenceAdapter: {
-        type: 'frozen',
-        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
-        defaultValue: null,
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bamLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.bai`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = configSchema;

package/dist/BamAdapter/index.d.ts

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

package/dist/BamAdapter/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 = BamAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BamAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'BamAdapter',
-            displayName: 'BAM adapter',
-            configSchema: configSchema_1.default,
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,53 +0,0 @@
-import { IndexedCramFile } from '@gmod/cram';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-import type { FilterBy } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-import type { BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-interface Header {
-    idToName?: string[];
-    nameToId?: Record<string, number>;
-    readGroups?: (string | undefined)[];
-}
-export default class CramAdapter extends BaseFeatureDataAdapter {
-    samHeader: Header;
-    private setupP?;
-    private configureP?;
-    private ultraLongFeatureCache;
-    private seqIdToRefName;
-    private seqIdToOriginalRefName;
-    configurePre(): Promise<{
-        cram: IndexedCramFile;
-        sequenceAdapter: BaseSequenceAdapter;
-    }>;
-    configure(): Promise<{
-        cram: IndexedCramFile;
-        sequenceAdapter: BaseSequenceAdapter;
-    }>;
-    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
-    private seqFetch;
-    private setupPre;
-    private setupPre2;
-    setup(opts?: BaseOptions): Promise<{
-        samHeader: Header;
-        cram: IndexedCramFile;
-        sequenceAdapter: BaseSequenceAdapter;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    refNameToId(refName: string): number | undefined;
-    refIdToName(refId: number): string | undefined;
-    refIdToOriginalName(refId: number): string | undefined;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions & {
-        filterBy: FilterBy;
-    }): import("rxjs").Observable<Feature>;
-    cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
-    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: number;
-        fetchSizeLimit: any;
-    }>;
-    private bytesForRegions;
-}
-export {};