@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -1,103 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { Instance } from 'mobx-state-tree';
-export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
-        showCoordinatesSetting: string;
-        intronBp: number;
-        upDownBp: number;
-        upperCaseCDS: boolean;
-        charactersPerRow: number;
-        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
-    } & {
-        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-        setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
-        setUpperCaseCDS(f: boolean): void;
-        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
-    } & {
-        readonly showCoordinates: boolean;
-        readonly showGenomicCoordsOption: boolean;
-        readonly hasCDS: boolean | undefined;
-        readonly hasExon: boolean | undefined;
-        readonly hasExonOrCDS: boolean | undefined;
-    } & {
-        afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
-}, {
-    error: unknown;
-} & {
-    setFeatureData(featureData: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-    clearFeatureData(): void;
-    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, {
-    type: "BaseFeatureWidget";
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
-        showCoordinatesSetting: string;
-        intronBp: number;
-        upDownBp: number;
-        upperCaseCDS: boolean;
-        charactersPerRow: number;
-        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
-    } & {
-        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-        setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
-        setUpperCaseCDS(f: boolean): void;
-        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
-    } & {
-        readonly showCoordinates: boolean;
-        readonly showGenomicCoordsOption: boolean;
-        readonly hasCDS: boolean | undefined;
-        readonly hasExon: boolean | undefined;
-        readonly hasExonOrCDS: boolean | undefined;
-    } & {
-        afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
-    id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    trackId: string | undefined;
-    trackType: string | undefined;
-    maxDepth: number | undefined;
-    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
-    formattedFields: any;
-    descriptions: Record<string, unknown> | undefined;
-    finalizedFeatureData: any;
-} & import("mobx-state-tree")._NotCustomized>;
-export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
-export type AlignmentFeatureWidgetModel = Instance<AlignmentFeatureWidgetStateModel>;

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = stateModelFactory;
-const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types.compose((0, BaseFeatureWidget_1.stateModelFactory)(pluginManager), mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
-        type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
-    }));
-}

package/dist/AlignmentsFeatureDetail/tagInfo.d.ts

@@ -1,63 +0,0 @@
-export declare const tags: {
-    AM: string;
-    AS: string;
-    BC: string;
-    BQ: string;
-    BZ: string;
-    CB: string;
-    CC: string;
-    CM: string;
-    CO: string;
-    CP: string;
-    CQ: string;
-    CR: string;
-    CS: string;
-    CT: string;
-    CY: string;
-    E2: string;
-    FI: string;
-    FS: string;
-    FZ: string;
-    GC: string;
-    GQ: string;
-    GS: string;
-    H0: string;
-    H1: string;
-    H2: string;
-    HI: string;
-    IH: string;
-    LB: string;
-    MC: string;
-    MD: string;
-    MF: string;
-    MI: string;
-    ML: string;
-    MM: string;
-    MQ: string;
-    NH: string;
-    NM: string;
-    OA: string;
-    OC: string;
-    OP: string;
-    OQ: string;
-    OX: string;
-    PG: string;
-    PQ: string;
-    PT: string;
-    PU: string;
-    Q2: string;
-    QT: string;
-    QX: string;
-    R2: string;
-    RG: string;
-    RT: string;
-    RX: string;
-    S2: string;
-    SA: string;
-    SM: string;
-    SQ: string;
-    TC: string;
-    TS: string;
-    U2: string;
-    UQ: string;
-};

package/dist/AlignmentsFeatureDetail/tagInfo.js

@@ -1,66 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.tags = void 0;
-exports.tags = {
-    AM: 'The smallest template-independent mapping quality in the template',
-    AS: 'Alignment score generated by aligner',
-    BC: 'Barcode sequence identifying the sample',
-    BQ: 'Offset to base alignment quality (BAQ)',
-    BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',
-    CB: 'Cell identifier',
-    CC: 'Reference name of the next hit',
-    CM: 'Edit distance between the color sequence and the color reference (see also {NM})',
-    CO: 'Free-text comments',
-    CP: 'Leftmost coordinate of the next hit',
-    CQ: 'Color read base qualities',
-    CR: 'Cellular barcode sequence bases (uncorrected)',
-    CS: 'Color read sequence',
-    CT: 'Complete read annotation tag, used for consensus annotation dummy features',
-    CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',
-    E2: 'The 2nd most likely base calls',
-    FI: 'The index of segment in the template',
-    FS: 'Segment suffix',
-    FZ: 'Flow stopToken intensities',
-    GC: 'Reserved for backwards compatibility reasons',
-    GQ: 'Reserved for backwards compatibility reasons',
-    GS: 'Reserved for backwards compatibility reasons',
-    H0: 'Number of perfect hits',
-    H1: 'Number of 1-difference hits (see also {NM})',
-    H2: 'Number of 2-difference hits',
-    HI: 'Query hit index',
-    IH: 'Query hit total count',
-    LB: 'Library',
-    MC: 'CIGAR string for mate/next segment',
-    MD: 'String encoding mismatched and deleted reference bases',
-    MF: 'Reserved for backwards compatibility reasons',
-    MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',
-    ML: 'Base modification probabilities',
-    MM: 'Base modifications / methylation ',
-    MQ: 'Mapping quality of the mate/next segment',
-    NH: 'Number of reported alignments that contain the query in the current record',
-    NM: 'Edit distance to the reference',
-    OA: 'Original alignment',
-    OC: 'Original CIGAR (deprecated; use {OA} instead)',
-    OP: 'Original mapping position (deprecated; use {OA} instead)',
-    OQ: 'Original base quality',
-    OX: 'Original unique molecular barcode bases',
-    PG: 'Program',
-    PQ: 'Phred likelihood of the template',
-    PT: 'Read annotations for parts of the padded read sequence',
-    PU: 'Platform unit',
-    Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',
-    QT: 'Phred quality of the sample barcode sequence in the {BC} tag',
-    QX: 'Quality score of the unique molecular identifier in the {RX} tag',
-    R2: 'Sequence of the mate/next segment in the template',
-    RG: 'Read group',
-    RT: 'Reserved for backwards compatibility reasons',
-    RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',
-    S2: 'Reserved for backwards compatibility reasons',
-    SA: 'Other canonical alignments in a chimeric alignment',
-    SM: 'Template-independent mapping quality',
-    SQ: 'Reserved for backwards compatibility reasons',
-    TC: 'The number of segments in the template',
-    TS: 'Transcript strand',
-    U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',
-    UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',
-};

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -1,6 +0,0 @@
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getTag(tag: string, feat: {
-    tags?: Record<string, unknown>;
-    [key: string]: unknown;
-}): unknown;
-export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/dist/AlignmentsFeatureDetail/util.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTag = getTag;
-exports.navToLoc = navToLoc;
-const util_1 = require("@jbrowse/core/util");
-function getTag(tag, feat) {
-    var _a;
-    return ((_a = feat.tags) === null || _a === void 0 ? void 0 : _a[tag]) || feat[tag];
-}
-async function navToLoc(locString, model) {
-    const session = (0, util_1.getSession)(model);
-    const { view } = model;
-    try {
-        if (view) {
-            await view.navToLocString(locString);
-        }
-        else {
-            throw new Error('No view associated with this view anymore');
-        }
-    }
-    catch (e) {
-        console.error(e);
-        session.notify(`${e}`);
-    }
-}

package/dist/AlignmentsTrack/configSchemaF.d.ts

@@ -1,79 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: string[];
-    };
-    description: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    category: {
-        description: string;
-        type: string;
-        defaultValue: never[];
-    };
-    metadata: {
-        type: string;
-        description: string;
-        defaultValue: {};
-    };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexingAttributes: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        indexingFeatureTypesToExclude: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        feature: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        subfeatures: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        depth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        maxDepth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        config: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        hideUris: {
-            type: string;
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/dist/AlignmentsTrack/configSchemaF.js

@@ -1,11 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = configSchemaFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-function x() { }
-function configSchemaFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
-        baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
-    });
-}

package/dist/AlignmentsTrack/index.d.ts

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

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;
-}