@jbrowse/plugin-alignments 2.17.0 → 2.18.0

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/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 {};

package/dist/CramAdapter/CramAdapter.js

@@ -4,28 +4,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const cram_1 = require("@gmod/cram");
-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 CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
+const util_2 = require("../shared/util");
 class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.samHeader = {};
-        // 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 fairly intensive but can reduce recomputation on
-        // these objects
         this.ultraLongFeatureCache = new QuickLRU_1.default({
             maxSize: 500,
         });
-        // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
     async configurePre() {
@@ -65,13 +60,13 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return cram.cram.getHeaderText();
     }
     async seqFetch(seqId, start, end) {
-        start -= 1; // convert from 1-based closed to interbase
+        start -= 1;
         const { sequenceAdapter } = await this.configure();
         const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
         if (!refName) {
             throw new Error('unknown');
         }
-        const seqChunks = await (0, rxjs_1.firstValueFrom)(sequenceAdapter
+        const seqChunks = await (0, rxjs_2.firstValueFrom)(sequenceAdapter
             .getFeatures({
             refName,
             start,
@@ -103,8 +98,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const conf = await this.configure();
             const { cram } = conf;
             const samHeader = await cram.cram.getSamHeader();
-            // use the @SQ lines in the header to figure out the
-            // mapping between ref ID numbers and names
             const idToName = [];
             const nameToId = {};
             samHeader
@@ -141,8 +134,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return samHeader.idToName;
     }
-    // use info from the SAM header if possible, but fall back to using
-    // the ref seq order from when the browser's refseqs were loaded
     refNameToId(refName) {
         if (this.samHeader.nameToId) {
             return this.samHeader.nameToId[refName];
@@ -152,8 +143,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return undefined;
     }
-    // use info from the SAM header if possible, but fall back to using
-    // the ref seq order from when the browser's refseqs were loaded
     refIdToName(refId) {
         var _a, _b;
         return ((_a = this.samHeader.idToName) === null || _a === void 0 ? void 0 : _a[refId]) || ((_b = this.seqIdToRefName) === null || _b === void 0 ? void 0 : _b[refId]);
@@ -162,9 +151,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.seqIdToOriginalRefName[refId];
     }
     getFeatures(region, opts) {
-        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
-        return (0, rxjs_2.ObservableCreate)(async (observer) => {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { cram, samHeader } = await this.setup(opts);
             const refId = this.refNameToId(refName);
             if (refId === undefined) {
@@ -176,25 +165,19 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
             const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
-            (0, util_1.checkAbortSignal)(signal);
+            (0, stopToken_1.checkStopToken)(stopToken);
             await (0, util_1.updateStatus)('Processing alignments', statusCallback, () => {
                 var _a;
                 const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
                 for (const record of records) {
-                    const flags = record.flags;
-                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                    if ((0, util_2.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
                         continue;
                     }
-                    if (tagFilter) {
-                        const readVal = tagFilter.tag === 'RG'
+                    if (tagFilter &&
+                        (0, util_2.filterTagValue)(tagFilter.tag === 'RG'
                             ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
-                            : record.tags[tagFilter.tag];
-                        const filterVal = tagFilter.value;
-                        if (filterVal === '*'
-                            ? readVal === undefined
-                            : `${readVal}` !== `${filterVal}`) {
-                            continue;
-                        }
+                            : record.tags[tagFilter.tag], tagFilter.value)) {
+                        continue;
                     }
                     if (readName && record.readName !== readName) {
                         continue;
@@ -211,13 +194,12 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
                 observer.complete();
             });
-        }, signal);
+        }, stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
     cramRecordToFeature(record) {
         return new CramSlightlyLazyFeature_1.default(record, this);
     }
-    // we return the configured fetchSizeLimit, and the bytes for the region
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
@@ -226,11 +208,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fetchSizeLimit,
         };
     }
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
     async bytesForRegions(regions, _opts) {
         const { cram } = await this.configure();
         const blockResults = await Promise.all(regions.map(region => {

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,6 +1,6 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { CramRecord } from '@gmod/cram';
-import CramAdapter from './CramAdapter';
+import type CramAdapter from './CramAdapter';
+import type { CramRecord } from '@gmod/cram';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -3,8 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("./util");
 const util_2 = require("../shared/util");
 class CramSlightlyLazyFeature {
-    // uses parameter properties to automatically create fields on the class
-    // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
     constructor(record, _store) {
         this.record = record;
         this._store = _store;
@@ -68,7 +66,6 @@ class CramSlightlyLazyFeature {
     get seq() {
         return this.record.getReadBases();
     }
-    // generate a CIGAR, based on code from jkbonfield
     get CIGAR() {
         return (0, util_1.readFeaturesToCIGAR)(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
@@ -92,18 +89,6 @@ class CramSlightlyLazyFeature {
     }
     get mismatches() {
         return (0, util_1.readFeaturesToMismatches)(this.record.readFeatures, this.start, this.qualRaw);
-        // this commented code can try to resolve MD tags, xref https://github.com/galaxyproject/tools-iuc/issues/6523#issuecomment-2462927211 but put on hold
-        // return this.tags.MD && this.seq
-        //   ? mismatches.concat(
-        //       mdToMismatches(
-        //         this.tags.MD,
-        //         parseCigar(this.CIGAR),
-        //         mismatches,
-        //         this.seq,
-        //         this.qualRaw,
-        //       ),
-        //     )
-        //   : mismatches
     }
     get fields() {
         return {
@@ -128,9 +113,7 @@ class CramSlightlyLazyFeature {
     toJSON() {
         return {
             ...this.fields,
-            // lazy
             CIGAR: this.CIGAR,
-            // lazy
             qual: this.qual,
         };
     }

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -1,7 +1,7 @@
-import { GenericFilehandle } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { Observable } from 'rxjs';
+import type { GenericFilehandle } from 'generic-filehandle';
 export declare function parseSmallFasta(text: string): {
     id: string;
     description: string;

package/dist/CramAdapter/CramTestAdapters.js

@@ -5,11 +5,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SequenceAdapter = exports.FetchableSmallFasta = void 0;
 exports.parseSmallFasta = parseSmallFasta;
-const rxjs_1 = require("rxjs");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const configuration_1 = require("@jbrowse/core/configuration");
-// setup for Cram Adapter Testing
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const rxjs_1 = require("rxjs");
 function parseSmallFasta(text) {
     return text
         .split('>')
@@ -81,6 +80,6 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return { unsubscribe: () => { } };
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.SequenceAdapter = SequenceAdapter;

package/dist/CramAdapter/configSchema.d.ts

@@ -1,15 +1,9 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot fetchSizeLimit
-     */
     fetchSizeLimit: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot cramLocation
-     */
     cramLocation: {
         type: string;
         defaultValue: {
@@ -17,9 +11,6 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot craiLocation
-     */
     craiLocation: {
         type: string;
         defaultValue: {
@@ -27,11 +18,6 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot sequenceAdapter
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: string;
         description: string;

package/dist/CramAdapter/configSchema.js

@@ -1,23 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config CramAdapter
- * used to configure CRAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
-    /**
-     * #slot fetchSizeLimit
-     */
     fetchSizeLimit: {
         type: 'number',
         description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
         defaultValue: 3000000,
     },
-    /**
-     * #slot cramLocation
-     */
     cramLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -25,9 +15,6 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot craiLocation
-     */
     craiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -35,11 +22,6 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot sequenceAdapter
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: 'frozen',
         description: 'sequence data adapter',

package/dist/CramAdapter/index.d.ts

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

package/dist/CramAdapter/index.js

@@ -28,7 +28,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = CramAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {

package/dist/CramAdapter/util.d.ts

@@ -1,5 +1,5 @@
-import { CramRecord } from '@gmod/cram';
-import { Mismatch } from '../shared/types';
+import type { Mismatch } from '../shared/types';
+import type { CramRecord } from '@gmod/cram';
 type ReadFeatures = CramRecord['readFeatures'];
 export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
 export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {