@jbrowse/plugin-alignments 2.17.0 → 3.0.0

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() {
@@ -34,7 +29,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
             cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
-            index: new cram_1.CraiIndex({ filehandle: (0, io_1.openLocation)(craiLocation, pm) }),
+            index: new cram_1.CraiIndex({
+                filehandle: (0, io_1.openLocation)(craiLocation, pm),
+            }),
             seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
         });
@@ -65,13 +62,13 @@ 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 +100,6 @@ 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
@@ -122,7 +117,10 @@ class CramAdapter extends BaseAdapter_1.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) {
@@ -141,8 +139,6 @@ 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 +148,6 @@ 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 +156,9 @@ 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 +170,19 @@ 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 +199,12 @@ 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 +213,6 @@ 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-filehandle2';
 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('>')
@@ -29,7 +28,8 @@ function parseSmallFasta(text) {
 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);
         });
     }
@@ -81,6 +81,6 @@ 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

@@ -15,20 +15,29 @@ 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 };
 };
 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?: {

package/dist/CramAdapter/util.js

@@ -26,7 +26,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
         }
         refPos = p - 1 - start;
         if (code === 'X') {
-            // substitution
             mismatches[j++] = {
                 start: refPos,
                 length: 1,
@@ -37,7 +36,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'I') {
-            // insertion
             mismatches[j++] = {
                 start: refPos,
                 type: 'insertion',
@@ -46,7 +44,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'N') {
-            // reference skip
             mismatches[j++] = {
                 type: 'skip',
                 length: data,
@@ -55,7 +52,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'S') {
-            // soft clip
             const len = data.length;
             mismatches[j++] = {
                 start: refPos,
@@ -66,10 +62,8 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'P') {
-            // padding
         }
         else if (code === 'H') {
-            // hard clip
             const len = data;
             mismatches[j++] = {
                 start: refPos,
@@ -80,7 +74,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'D') {
-            // deletion
             mismatches[j++] = {
                 type: 'deletion',
                 length: data,
@@ -89,21 +82,15 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'b') {
-            // stretch of bases
         }
         else if (code === 'q') {
-            // stretch of qual scores
         }
         else if (code === 'B') {
-            // a pair of [base, qual]
         }
         else if (code === 'i') {
-            // single-base insertion, we collect these if there are multiple in a row
-            // into a single insertion entry
             insLen++;
         }
         else if (code === 'Q') {
-            // single quality value
         }
     }
     if (sublen && insLen > 0) {
@@ -125,7 +112,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     if (!refRegion) {
         return '';
     }
-    // not sure I should access these, but...
     const ref = refRegion.seq;
     const refStart = refRegion.start;
     let lastPos = alignmentStart;
@@ -149,7 +135,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen += sublen;
             }
             if (code === 'b') {
-                // An array of bases stored verbatim
                 const ret = data.split(',');
                 const added = String.fromCharCode(...ret);
                 seq += added;
@@ -157,19 +142,16 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen += added.length;
             }
             else if (code === 'B') {
-                // Single base (+ qual score)
                 seq += sub;
                 lastPos++;
                 oplen++;
             }
             else if (code === 'X') {
-                // Substitution
                 seq += sub;
                 lastPos++;
                 oplen++;
             }
             else if (code === 'D' || code === 'N') {
-                // Deletion or Ref Skip
                 lastPos += data;
                 if (oplen) {
                     cigar += `${oplen}${op}`;
@@ -178,7 +160,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'I' || code === 'S') {
-                // Insertion or soft-clip
                 seq += data;
                 if (oplen) {
                     cigar += `${oplen}${op}`;
@@ -187,8 +168,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'i') {
-                // Single base insertion
-                // seq += data
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
@@ -197,20 +176,18 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'P') {
-                // Padding
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
                 cigar += `${data}P`;
             }
             else if (code === 'H') {
-                // Hard clip
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
                 cigar += `${data}H`;
                 oplen = 0;
-            } // else q or Q
+            }
         }
     }
     else {

package/dist/GuessAlignmentsTypes/index.d.ts

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

package/dist/GuessAlignmentsTypes/index.js

@@ -1,48 +1,33 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = GuessAlignmentsTypesF;
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.cram$/i;
-            const adapterName = 'CramAdapter';
-            const fileName = (0, tracks_1.getFileName)(file);
-            const obj = {
-                type: adapterName,
-                cramLocation: file,
-                craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
-            }
-            if (adapterHint === adapterName) {
-                return obj;
-            }
-            return adapterGuesser(file, index, adapterHint);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.bam$/i;
-            const adapterName = 'BamAdapter';
             const fileName = (0, tracks_1.getFileName)(file);
             const indexName = index && (0, tracks_1.getFileName)(index);
-            const obj = {
-                type: adapterName,
-                bamLocation: file,
-                index: {
-                    location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if ((0, util_1.testAdapter)(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
+                return {
+                    type: 'BamAdapter',
+                    bamLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
+                    },
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
+                return {
+                    type: 'CramAdapter',
+                    cramLocation: file,
+                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,6 +1,6 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
+import type { BamFile } from '@gmod/bam';
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
     protected configurePre(): Promise<{
         bam: BamFile;

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,23 +1,14 @@
 declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     htsgetBase: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     htsgetTrackId: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         description: string;