@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.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 = SupplementaryAlignments;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const util_1 = require("@jbrowse/core/util");
-const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
-const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
-function SupplementaryAlignments(props) {
-    const { model, tag, feature } = props;
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    let hasBreakendSplitView = false;
-    try {
-        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
-    }
-    catch (e) {
-    }
-    return ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Supplementary alignments", children: [(0, jsx_runtime_1.jsx)(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }), hasBreakendSplitView ? ((0, jsx_runtime_1.jsx)(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null] }));
-}

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,5 +0,0 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
-    tag: string;
-    model: AlignmentFeatureWidgetModel;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SupplementaryAlignmentsLocStrings;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-const MismatchParser_1 = require("../MismatchParser");
-const util_1 = require("./util");
-function SupplementaryAlignmentsLocStrings({ tag, model, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "List of supplementary alignment locations" }), (0, jsx_runtime_1.jsx)("ul", { children: tag
-                    .split(';')
-                    .filter(SA => !!SA)
-                    .map((SA, idx) => {
-                    const [saRef, saStart, saStrand, saCigar] = SA.split(',');
-                    const saLength = (0, MismatchParser_1.getLengthOnRef)(saCigar);
-                    const extra = Math.floor(saLength / 5);
-                    const start = +saStart;
-                    const end = +saStart + saLength;
-                    const sp = start - extra;
-                    const ep = end + extra;
-                    const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
-                    const displayStart = start.toLocaleString('en-US');
-                    const displayEnd = end.toLocaleString('en-US');
-                    const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-                    return ((0, jsx_runtime_1.jsx)("li", { children: (0, jsx_runtime_1.jsx)(material_1.Link, { href: "#", onClick: async (event) => {
-                                event.preventDefault();
-                                (0, util_1.navToLoc)(locString, model);
-                            }, children: displayString }) }, `${locString}-${idx}`));
-                }) })] }));
-}

package/dist/AlignmentsFeatureDetail/configSchema.d.ts

@@ -1 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/AlignmentsFeatureDetail/configSchema.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('AlignmentsFeatureWidget', {});

package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts

@@ -1,23 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export interface ReducedFeature {
-    refName: string;
-    start: number;
-    clipPos: number;
-    end: number;
-    strand: number;
-    seqLength: number;
-    syntenyId?: number;
-    uniqueId: string;
-    mate: {
-        refName: string;
-        start: number;
-        end: number;
-        syntenyId?: number;
-        uniqueId?: string;
-    };
-}
-export declare function getSAFeatures({ view, feature, }: {
-    view: LinearGenomeViewModel;
-    feature: Feature;
-}): Promise<ReducedFeature[]>;

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSAFeatures = getSAFeatures;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
-async function getSAFeatures({ view, feature, }) {
-    var _a;
-    const { assemblyManager } = (0, util_1.getSession)(view);
-    const cigar = feature.get('CIGAR');
-    const origStrand = feature.get('strand');
-    const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
-    const readName = feature.get('name');
-    const clipPos = (0, MismatchParser_1.getClip)(cigar, 1);
-    const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
-    if (!assembly) {
-        throw new Error('assembly not found');
-    }
-    const suppAlns = (0, MismatchParser_1.featurizeSA)(SA, feature.id(), origStrand, readName, true);
-    const feat = feature.toJSON();
-    feat.clipPos = clipPos;
-    feat.strand = 1;
-    feat.mate = {
-        refName: readName,
-        start: clipPos,
-        end: clipPos + (0, MismatchParser_1.getLengthSansClipping)(cigar),
-    };
-    const features = [feat, ...suppAlns];
-    for (const [idx, f] of features.entries()) {
-        f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
-        f.syntenyId = idx;
-        f.mate.syntenyId = idx;
-        f.mate.uniqueId = `${f.uniqueId}_mate`;
-    }
-    features.sort((a, b) => a.clipPos - b.clipPos);
-    return features;
-}

package/dist/AlignmentsFeatureDetail/index.d.ts

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

package/dist/AlignmentsFeatureDetail/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 = AlignmentFeatureDetailsF;
-const react_1 = require("react");
-const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const configSchema_1 = require("./configSchema");
-const stateModelFactory_1 = require("./stateModelFactory");
-function AlignmentFeatureDetailsF(pluginManager) {
-    pluginManager.addWidgetType(() => new WidgetType_1.default({
-        name: 'AlignmentsFeatureWidget',
-        heading: 'Feature details',
-        configSchema: configSchema_1.configSchema,
-        stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
-        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AlignmentsFeatureDetail')))),
-    }));
-}

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,22 +0,0 @@
-import type { ReducedFeature } from './getSAFeatures';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function getBreakpointSplitView({ f1, f2, view, }: {
-    f1: ReducedFeature;
-    f2: ReducedFeature;
-    view: LinearGenomeViewModel;
-}): {
-    type: string;
-    views: {
-        type: string;
-        displayedRegions: {
-            start: number;
-            end: number;
-            refName: string;
-            assemblyName: string;
-        }[];
-        hideHeader: boolean;
-        bpPerPx: number;
-        offsetPx: number;
-    }[];
-    displayName: string;
-};

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBreakpointSplitView = getBreakpointSplitView;
-const util_1 = require("@jbrowse/core/util");
-function getBreakpointSplitView({ f1, f2, view, }) {
-    const { assemblyName } = view.displayedRegions[0];
-    const { assemblyManager } = (0, util_1.getSession)(view);
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    if (!assembly.regions) {
-        throw new Error(`assembly ${assemblyName} regions not loaded`);
-    }
-    const topRegion = assembly.regions.find(f => f.refName === f1.refName);
-    const bottomRegion = assembly.regions.find(f => f.refName === f2.refName);
-    if (!topRegion || !bottomRegion) {
-        throw new Error('unable to find the refName for the top or bottom of the breakpoint view');
-    }
-    const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
-    const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
-    const s = f1.strand === 1 ? f1.end : f1.start;
-    const e = f2.strand === 1 ? f2.start : f2.end;
-    topMarkedRegion[0].end = s;
-    topMarkedRegion[1].start = s + 1;
-    bottomMarkedRegion[0].end = e;
-    bottomMarkedRegion[1].start = e + 1;
-    const bpPerPx = 10;
-    return {
-        type: 'BreakpointSplitView',
-        views: [
-            {
-                type: 'LinearGenomeView',
-                displayedRegions: topMarkedRegion,
-                hideHeader: true,
-                bpPerPx,
-                offsetPx: (topRegion.start + s) / bpPerPx,
-            },
-            {
-                type: 'LinearGenomeView',
-                displayedRegions: bottomMarkedRegion,
-                hideHeader: true,
-                bpPerPx,
-                offsetPx: (bottomRegion.start + e) / bpPerPx,
-            },
-        ],
-        displayName: 'breakend split detail',
-    };
-}

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: string;
-    } & {
-        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: string): 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: string;
-    } & {
-        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: string): 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;