@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
     tag: string;
     model: AlignmentFeatureWidgetModel;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,39 +1,29 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignmentsLocStrings;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
-// locals
 const MismatchParser_1 = require("../MismatchParser");
 const util_1 = require("./util");
 function SupplementaryAlignmentsLocStrings({ tag, model, }) {
-    return (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "List of supplementary alignment locations"),
-        react_1.default.createElement("ul", null, 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 (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            react_1.default.createElement("li", { key: `${locString}-${idx}` },
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: async (event) => {
-                        event.preventDefault();
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                        (0, util_1.navToLoc)(locString, model);
-                    } }, displayString)));
-        }))));
+    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/getSAFeatures.d.ts

@@ -1,5 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export interface ReducedFeature {
     refName: string;
     start: number;

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getSAFeatures = getSAFeatures;
 const util_1 = require("@jbrowse/core/util");
-// locals
 const MismatchParser_1 = require("../MismatchParser");
 async function getSAFeatures({ view, feature, }) {
     var _a;
@@ -12,9 +11,6 @@ async function getSAFeatures({ view, feature, }) {
     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);
-    // get the canonical refname for the read because if the read.get('refName')
-    // is chr1 and the actual fasta refName is 1 then no tracks can be opened on
-    // the top panel of the linear read vs ref
     const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
     if (!assembly) {
         throw new Error('assembly not found');

package/dist/AlignmentsFeatureDetail/index.d.ts

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

package/dist/AlignmentsFeatureDetail/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,5 +1,5 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ReducedFeature } from './getSAFeatures';
+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;

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { Instance } from 'mobx-state-tree';
+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">;

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
     const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
     return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {

package/dist/AlignmentsFeatureDetail/tagInfo.js

@@ -20,7 +20,7 @@ exports.tags = {
     E2: 'The 2nd most likely base calls',
     FI: 'The index of segment in the template',
     FS: 'Segment suffix',
-    FZ: 'Flow signal intensities',
+    FZ: 'Flow stopToken intensities',
     GC: 'Reserved for backwards compatibility reasons',
     GQ: 'Reserved for backwards compatibility reasons',
     GS: 'Reserved for backwards compatibility reasons',

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -1,4 +1,4 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
     tags?: Record<string, unknown>;
     [key: string]: unknown;

package/dist/AlignmentsTrack/configSchemaF.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+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;

package/dist/AlignmentsTrack/configSchemaF.js

@@ -3,16 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = configSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 function configSchemaFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
     });
 }

package/dist/AlignmentsTrack/index.d.ts

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

package/dist/AlignmentsTrack/index.js

@@ -17,9 +17,6 @@ function register(pm) {
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'AlignmentsTrack', configSchema),
         });
         const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay');
-        // Add LinearAlignmentsDisplay here so that it has priority over the other
-        // linear displays (defaults to order the displays are added, but we have
-        // to add the Pileup and SNPCoverage displays first).
         track.addDisplayType(linearAlignmentsDisplay);
         return track;
     });

package/dist/BamAdapter/BamAdapter.d.ts

@@ -1,8 +1,9 @@
 import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { FilterBy } from '../shared/types';
+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>;
@@ -23,7 +24,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;

package/dist/BamAdapter/BamAdapter.js

@@ -4,29 +4,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bam_1 = require("@gmod/bam");
-const operators_1 = require("rxjs/operators");
-const rxjs_1 = require("rxjs");
-// jbrowse
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_2 = require("@jbrowse/core/util/rxjs");
 const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-// locals
+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);
-        // used for avoiding re-creation new BamSlightlyLazyFeatures, keeping
-        // mismatches in cache. at an average of 100kb-300kb, keeping even just 500
-        // of these in memory is memory intensive but can reduce recomputation on
-        // these objects
         this.ultraLongFeatureCache = new QuickLRU_1.default({
             maxSize: 500,
         });
     }
-    // derived classes may not use the same configuration so a custom configure
-    // method allows derived classes to override this behavior
     async configurePre() {
         const bamLocation = this.getConf('bamLocation');
         const location = this.getConf(['index', 'location']);
@@ -58,23 +52,20 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.configureP;
     }
-    async getHeader(opts) {
+    async getHeader(_opts) {
         const { bam } = await this.configure();
-        return bam.getHeaderText(opts);
+        return bam.getHeaderText();
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
         const { bam } = await this.configure();
         this.samHeader = await (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
-            const samHeader = await bam.getHeader(opts);
-            // use the @SQ lines in the header to figure out the
-            // mapping between ref ref ID numbers and names
+            const samHeader = await bam.getHeader();
             const idToName = [];
             const nameToId = {};
             samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
                 const SN = sqLine.data.find(item => item.tag === 'SN');
                 if (SN) {
-                    // this is the ref name
                     const refName = SN.value;
                     nameToId[refName] = refId;
                     idToName[refId] = refName;
@@ -112,7 +103,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             end,
             assemblyName: '',
         });
-        const seqChunks = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
+        const seqChunks = await (0, rxjs_2.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
         let sequence = '';
         seqChunks
             .sort((a, b) => a.get('start') - b.get('start'))
@@ -132,11 +123,13 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     getFeatures(region, opts) {
         const { refName, start, end, originalRefName } = region;
-        const { signal, filterBy, statusCallback = () => { } } = opts || {};
-        return (0, rxjs_2.ObservableCreate)(async (observer) => {
+        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
-            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, 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) {
@@ -144,25 +137,16 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     if (!record.tags.MD) {
                         ref = await this.seqFetch(originalRefName || refName, record.start, record.end);
                     }
-                    const flags = record.flags;
-                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                    if ((0, util_2.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
                         continue;
                     }
-                    if (tagFilter) {
-                        const readVal = record.tags[tagFilter.tag];
-                        const filterVal = tagFilter.value;
-                        if (filterVal === '*'
-                            ? readVal === undefined
-                            : `${readVal}` !== `${filterVal}`) {
-                            continue;
-                        }
+                    if (tagFilter &&
+                        (0, util_2.filterTagValue)(record.tags[tagFilter.tag], tagFilter.value)) {
+                        continue;
                     }
                     if (readName && record.name !== readName) {
                         continue;
                     }
-                    // retrieve a feature from our feature cache if it is available, the
-                    // features in the cache have pre-computed mismatches objects that
-                    // can be re-used across blocks
                     const ret = this.ultraLongFeatureCache.get(`${record.id}`);
                     if (!ret) {
                         const elt = new BamSlightlyLazyFeature_1.default(record, this, ref);
@@ -175,11 +159,10 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
                 observer.complete();
             });
-        }, signal);
+        });
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
-        // this is a method to avoid calling on htsget adapters
         if (bam.index) {
             const bytes = await (0, util_1.bytesForRegions)(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
@@ -187,8 +170,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return super.getMultiRegionFeatureDensityStats(regions, opts);
     }
-    freeResources( /* { region } */) { }
-    // depends on setup being called before the BAM constructor
+    freeResources() { }
     refIdToName(refId) {
         var _a;
         return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,6 +1,6 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { BamRecord } from '@gmod/bam';
-import BamAdapter from './BamAdapter';
+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;

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,11 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-// locals
 const MismatchParser_1 = require("../MismatchParser");
 const util_1 = require("../shared/util");
 class BamSlightlyLazyFeature {
-    // uses parameter properties to automatically create fields on the class
-    // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
     constructor(record, adapter, ref) {
         this.record = record;
         this.adapter = adapter;

package/dist/BamAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bamLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,19 +20,11 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     fetchSizeLimit: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: string;
         description: string;

package/dist/BamAdapter/configSchema.js

@@ -2,31 +2,18 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config BamAdapter
- * used to configure BAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
-    /**
-     * #slot
-     */
     bamLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('BamIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['BAI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'BAI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -35,19 +22,11 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
             },
         },
     }),
-    /**
-     * #slot
-     */
     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,
     },
-    /**
-     * #slot
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: 'frozen',
         description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',

package/dist/BamAdapter/index.d.ts

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

package/dist/BamAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,8 +1,10 @@
-import { IndexedCramFile, CramRecord } from '@gmod/cram';
-import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Region, Feature } from '@jbrowse/core/util';
+import { IndexedCramFile } from '@gmod/cram';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-import { FilterBy } from '../shared/types';
+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>;
@@ -42,11 +44,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         bytes: number;
         fetchSizeLimit: any;
     }>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
     private bytesForRegions;
 }
 export {};