@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/BamAdapter/BamAdapter.js

@@ -1,27 +1,21 @@
 import { BamFile } from '@gmod/bam';
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-// jbrowse
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
-// locals
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
+import { filterReadFlag, filterTagValue } from '../shared/util';
 export default class BamAdapter extends 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({
             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']);
@@ -53,23 +47,20 @@ export default class BamAdapter extends 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 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;
@@ -127,11 +118,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(region, opts) {
         const { refName, start, end, originalRefName } = region;
-        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
-            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            checkStopToken(stopToken);
+            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end));
+            checkStopToken(stopToken);
             await updateStatus('Processing alignments', statusCallback, async () => {
                 const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
                 for (const record of records) {
@@ -139,25 +132,16 @@ export default class BamAdapter extends 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 (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 &&
+                        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(record, this, ref);
@@ -170,11 +154,10 @@ export default class BamAdapter extends 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 bytesForRegions(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
@@ -182,8 +165,7 @@ export default class BamAdapter extends 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/esm/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/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,9 +1,6 @@
-// locals
 import { getMismatches } from '../MismatchParser';
 import { cacheGetter } from '../shared/util';
 export default 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/esm/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/esm/BamAdapter/configSchema.js

@@ -1,30 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config BamAdapter
- * used to configure BAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('BamAdapter', {
-    /**
-     * #slot
-     */
     bamLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('BamIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['BAI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'BAI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -33,19 +20,11 @@ const configSchema = 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/esm/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/esm/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/esm/CramAdapter/CramAdapter.js

@@ -1,26 +1,21 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-// jbrowse
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal, updateStatus, toLocale } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { toLocale, updateStatus } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
-// locals
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+import { filterReadFlag, filterTagValue } from '../shared/util';
 export default class CramAdapter extends 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({
             maxSize: 500,
         });
-        // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
     async configurePre() {
@@ -29,7 +24,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const cram = new IndexedCramFile({
             cramFilehandle: openLocation(cramLocation, pm),
-            index: new CraiIndex({ filehandle: openLocation(craiLocation, pm) }),
+            index: new CraiIndex({
+                filehandle: openLocation(craiLocation, pm),
+            }),
             seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
         });
@@ -60,7 +57,7 @@ export default class CramAdapter extends 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) {
@@ -98,8 +95,6 @@ export default class CramAdapter extends 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
@@ -117,7 +112,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                 .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
             const data = { idToName, nameToId, readGroups };
             this.samHeader = data;
-            return { samHeader: data, ...conf };
+            return {
+                samHeader: data,
+                ...conf,
+            };
         });
     }
     async setup(opts) {
@@ -136,8 +134,6 @@ export default class CramAdapter extends 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];
@@ -147,8 +143,6 @@ export default class CramAdapter extends 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]);
@@ -157,7 +151,7 @@ export default class CramAdapter extends 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 ObservableCreate(async (observer) => {
             const { cram, samHeader } = await this.setup(opts);
@@ -171,25 +165,19 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
             const records = await updateStatus('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
-            checkAbortSignal(signal);
+            checkStopToken(stopToken);
             await 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 (filterReadFlag(record.flags, flagInclude, flagExclude)) {
                         continue;
                     }
-                    if (tagFilter) {
-                        const readVal = tagFilter.tag === 'RG'
+                    if (tagFilter &&
+                        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;
@@ -206,13 +194,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                 }
                 observer.complete();
             });
-        }, signal);
+        }, stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
     cramRecordToFeature(record) {
         return new CramSlightlyLazyFeature(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');
@@ -221,11 +208,6 @@ export default class CramAdapter extends 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/esm/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/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,8 +1,6 @@
 import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util';
 import { cacheGetter } from '../shared/util';
 export default 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;
@@ -66,7 +64,6 @@ export default class CramSlightlyLazyFeature {
     get seq() {
         return this.record.getReadBases();
     }
-    // generate a CIGAR, based on code from jkbonfield
     get CIGAR() {
         return readFeaturesToCIGAR(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
@@ -90,18 +87,6 @@ export default class CramSlightlyLazyFeature {
     }
     get mismatches() {
         return 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 {
@@ -126,9 +111,7 @@ export default class CramSlightlyLazyFeature {
     toJSON() {
         return {
             ...this.fields,
-            // lazy
             CIGAR: this.CIGAR,
-            // lazy
             qual: this.qual,
         };
     }

package/esm/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-filehandle2';
 export declare function parseSmallFasta(text: string): {
     id: string;
     description: string;

package/esm/CramAdapter/CramTestAdapters.js

@@ -1,8 +1,7 @@
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-// setup for Cram Adapter Testing
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { Observable } from 'rxjs';
 export function parseSmallFasta(text) {
     return text
         .split('>')
@@ -22,7 +21,8 @@ export function parseSmallFasta(text) {
 export class FetchableSmallFasta {
     constructor(filehandle) {
         this.data = filehandle.readFile().then(buffer => {
-            const text = buffer.toString('utf8');
+            const decoder = new TextDecoder('utf8');
+            const text = decoder.decode(buffer);
             return parseSmallFasta(text);
         });
     }
@@ -73,5 +73,5 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
             return { unsubscribe: () => { } };
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/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/esm/CramAdapter/configSchema.js

@@ -1,21 +1,11 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config CramAdapter
- * used to configure CRAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = 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: {
@@ -23,9 +13,6 @@ const configSchema = ConfigurationSchema('CramAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot craiLocation
-     */
     craiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -33,11 +20,6 @@ const configSchema = 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/esm/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/esm/CramAdapter/index.js

@@ -1,5 +1,4 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-// locals
 import configSchema from './configSchema';
 export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {

package/esm/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?: {