@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/dist/AlignmentsTrack/index.d.ts

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

package/dist/AlignmentsTrack/index.js

@@ -6,18 +6,28 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+/**
+ * #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 configSchemaFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
+    return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
+    });
 }
-function register(pluginManager) {
-    pluginManager.addTrackType(() => {
-        const configSchema = configSchemaFactory(pluginManager);
+function register(pm) {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaFactory(pm);
         const track = new TrackType_1.default({
             name: 'AlignmentsTrack',
             configSchema,
-            stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'AlignmentsTrack', configSchema),
+            stateModel: (0, models_1.createBaseTrackModel)(pm, 'AlignmentsTrack', configSchema),
         });
-        const linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay');
+        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).

package/dist/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AACnD,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF,EAAE,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,iBAAiB,EACjB,YAAY,CACb;SACF,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,aAAa,CAAC,cAAc,CAC1D,yBAAyB,CAC1B,CAAA;QACD,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AArBD,2BAqBC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAfD,2BAeC"}

package/dist/BamAdapter/BamAdapter.d.ts

@@ -9,9 +9,13 @@ interface Header {
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
-    protected configured?: Promise<{
+    private configureP?;
+    protected configurePre(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter;
+        sequenceAdapter: BaseFeatureDataAdapter;
+    } | {
+        bam: BamFile;
+        sequenceAdapter?: undefined;
     }>;
     protected configure(): Promise<{
         bam: BamFile;

package/dist/BamAdapter/BamAdapter.js

@@ -9,43 +9,47 @@ const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
-const configuration_1 = require("@jbrowse/core/configuration");
 const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
 class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // 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']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const pm = this.pluginManager;
+        const csi = indexType === 'CSI';
+        const bam = new bam_1.BamFile({
+            bamFilehandle: (0, io_1.openLocation)(bamLocation, pm),
+            csiFilehandle: csi ? (0, io_1.openLocation)(location, pm) : undefined,
+            baiFilehandle: !csi ? (0, io_1.openLocation)(location, pm) : undefined,
+            // chunkSizeLimit and fetchSizeLimit are more troublesome than
+            // helpful, and have given overly large values on the ultra long
+            // nanopore reads even with 500MB limits, so disabled with infinity
+            chunkSizeLimit: Infinity,
+            fetchSizeLimit: Infinity,
+            yieldThreadTime: Infinity,
+        });
+        const adapterConfig = this.getConf('sequenceAdapter');
+        if (adapterConfig && this.getSubAdapter) {
+            const { dataAdapter } = await this.getSubAdapter(adapterConfig);
+            return {
+                bam,
+                sequenceAdapter: dataAdapter,
+            };
+        }
+        else {
+            return { bam };
+        }
+    }
     async configure() {
-        if (!this.configured) {
-            const bamLocation = (0, configuration_1.readConfObject)(this.config, 'bamLocation');
-            const location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
-            const indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
-            const bam = new bam_1.BamFile({
-                bamFilehandle: (0, io_1.openLocation)(bamLocation, this.pluginManager),
-                csiFilehandle: indexType === 'CSI'
-                    ? (0, io_1.openLocation)(location, this.pluginManager)
-                    : undefined,
-                baiFilehandle: indexType !== 'CSI'
-                    ? (0, io_1.openLocation)(location, this.pluginManager)
-                    : undefined,
-                // chunkSizeLimit and fetchSizeLimit are more troublesome than
-                // helpful, and have given overly large values on the ultra long
-                // nanopore reads even with 500MB limits, so disabled with infinity
-                chunkSizeLimit: Infinity,
-                fetchSizeLimit: Infinity,
-                yieldThreadTime: Infinity,
+        if (!this.configureP) {
+            this.configureP = this.configurePre().catch(e => {
+                this.configureP = undefined;
+                throw e;
             });
-            const adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-            if (adapterConfig && this.getSubAdapter) {
-                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => ({
-                    bam,
-                    sequenceAdapter: dataAdapter,
-                }));
-            }
-            else {
-                this.configured = Promise.resolve({ bam });
-            }
         }
-        return this.configured;
+        return this.configureP;
     }
     async getHeader(opts) {
         const { bam } = await this.configure();
@@ -161,7 +165,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         // @ts-ignore
         if (bam.index.filehandle !== '?') {
             const bytes = await (0, util_1.bytesForRegions)(regions, bam);
-            const fetchSizeLimit = (0, configuration_1.readConfObject)(this.config, 'fetchSizeLimit');
+            const fetchSizeLimit = this.getConf('fetchSizeLimit');
             return { bytes, fetchSizeLimit };
         }
         else {

package/dist/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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package/dist/BamAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/BamAdapter/configSchema.js

@@ -2,17 +2,31 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('BamAdapter', {
+/**
+ * #config BamAdapter
+ * used to configure BAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+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: {
@@ -21,13 +35,24 @@ exports.default = mobx_state_tree_1.types.late(() => (0, configuration_1.Configu
             },
         },
     }),
+    /**
+     * #slot
+     */
     fetchSizeLimit: {
         type: 'number',
+        description: 'used to determine when 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',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/BamAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IAED,KAAK,EAAE,IAAA,mCAAmB,EAAC,UAAU,EAAE;QACrC;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,qBAAqB;gBAC1B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,4FAA4F;QAC9F,YAAY,EAAE,OAAS;KACxB;IACD;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,YAAY,CAAA"}

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { IndexedCramFile, CramRecord } from '@gmod/cram';
+import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
-    readGroups?: number[];
+    readGroups?: (string | undefined)[];
 }
 interface FilterBy {
     flagInclude: number;
@@ -18,13 +19,18 @@ interface FilterBy {
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
+    private configureP?;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
+    configurePre(): Promise<{
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
+    }>;
     configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -38,9 +44,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
+        bytes: number;
         fetchSizeLimit: any;
     }>;
     /**

package/dist/CramAdapter/CramAdapter.js

@@ -17,7 +17,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
-    async configure() {
+    async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
         if (!cramLocation) {
@@ -26,38 +26,43 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         if (!craiLocation) {
             throw new Error('missing craiLocation argument');
         }
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
-            cramFilehandle: (0, io_1.openLocation)(cramLocation, this.pluginManager),
-            index: new cram_1.CraiIndex({
-                filehandle: (0, io_1.openLocation)(craiLocation, this.pluginManager),
-            }),
-            seqFetch: this.seqFetch.bind(this),
+            cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
+            index: new cram_1.CraiIndex({ filehandle: (0, io_1.openLocation)(craiLocation, pm) }),
+            seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
             fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
         });
-        // instantiate the sequence adapter
-        const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
         if (!this.getSubAdapter) {
             throw new Error('Error getting subadapter');
         }
         const seqConf = this.getConf('sequenceAdapter');
-        const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf);
-        if (!(sequenceAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter)) {
-            throw new Error(`CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`);
+        const subadapter = await this.getSubAdapter(seqConf);
+        return {
+            cram,
+            sequenceAdapter: subadapter.dataAdapter,
+        };
+    }
+    async configure() {
+        if (!this.configureP) {
+            this.configureP = this.configurePre().catch(e => {
+                this.configureP = undefined;
+                throw e;
+            });
         }
-        return { cram, sequenceAdapter };
+        return this.configureP;
     }
     async getHeader(opts) {
         const { cram } = await this.configure();
-        return cram.cram.getHeaderText(opts);
+        return cram.cram.getHeaderText();
     }
     async seqFetch(seqId, start, end) {
         start -= 1; // convert from 1-based closed to interbase
         const { sequenceAdapter } = await this.configure();
         const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
         if (!refName) {
-            return undefined;
+            throw new Error('unknown');
         }
         const seqChunks = await sequenceAdapter
             .getFeatures({
@@ -87,10 +92,10 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const configured = await this.configure();
+        const conf = await this.configure();
         statusCallback('Downloading index');
-        const { cram } = configured;
-        const samHeader = await cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+        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 = [];
@@ -113,7 +118,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const data = { idToName, nameToId, readGroups };
         statusCallback('');
         this.samHeader = data;
-        return { samHeader: data, ...configured };
+        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -145,13 +150,8 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // 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) {
-        if (this.samHeader.idToName) {
-            return this.samHeader.idToName[refId];
-        }
-        if (this.seqIdToRefName) {
-            return this.seqIdToRefName[refId];
-        }
-        return undefined;
+        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]);
     }
     refIdToOriginalName(refId) {
         return this.seqIdToOriginalRefName[refId];
@@ -160,44 +160,37 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { cram, sequenceAdapter } = await this.setup(opts);
-            statusCallback('Downloading alignments');
-            if (!this.seqIdToRefName) {
-                this.seqIdToRefName = await sequenceAdapter.getRefNames(opts);
-            }
+            const { cram } = await this.setup(opts);
             const refId = this.refNameToId(refName);
-            if (refId !== undefined) {
-                if (originalRefName) {
-                    this.seqIdToOriginalRefName[refId] = originalRefName;
-                }
-                const records = await cram.getRecordsForRange(refId, start, end, opts);
-                (0, util_1.checkAbortSignal)(signal);
-                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                let filtered = records.filter((record) => {
-                    const flags = record.flags;
-                    return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-                });
-                if (tagFilter) {
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    filtered = filtered.filter((record) => {
-                        const val = record[tagFilter.tag];
-                        return val === '*' ? val !== undefined : val === tagFilter.value;
-                    });
-                }
-                if (readName) {
-                    filtered = filtered.filter(
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    (record) => record.readName === readName);
-                }
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                filtered.forEach((record) => {
-                    observer.next(this.cramRecordToFeature(record));
+            if (refId === undefined) {
+                console.warn('Unknown refName', refName);
+                observer.complete();
+                return;
+            }
+            if (originalRefName) {
+                this.seqIdToOriginalRefName[refId] = originalRefName;
+            }
+            statusCallback('Downloading alignments');
+            const records = await cram.getRecordsForRange(refId, start, end);
+            (0, util_1.checkAbortSignal)(signal);
+            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+            let filtered = records.filter(record => {
+                const flags = record.flags;
+                return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
+            });
+            if (tagFilter) {
+                filtered = filtered.filter(record => {
+                    // @ts-ignore
+                    const val = record[tagFilter.tag];
+                    return val === '*' ? val !== undefined : val === tagFilter.value;
                 });
             }
-            else {
-                console.warn('Unknown refName', refName);
+            if (readName) {
+                filtered = filtered.filter(record => record.readName === readName);
             }
+            filtered.forEach(record => {
+                observer.next(this.cramRecordToFeature(record));
+            });
             statusCallback('');
             observer.complete();
         }, signal);
@@ -225,7 +218,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const blockResults = await Promise.all(regions.map(region => {
             const { refName, start, end } = region;
             const chrId = this.refNameToId(refName);
-            return cram.index.getEntriesForRange(chrId, start, end);
+            return chrId !== undefined
+                ? cram.index.getEntriesForRange(chrId, start, end)
+                : [{ sliceBytes: 0 }];
         }));
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }

package/dist/CramAdapter/CramAdapter.js.map

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+{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAAsE;AACtE,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAuQ/C,CAAC;IArQQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,sBAAe,CAAC;YAC/B,cAAc,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,gBAAS,CAAC,EAAE,UAAU,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,eAAe;aACpC,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;aACf,SAAS,EAAE,CAAA;QAEd,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QAC/C,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACnC,cAAc,CAAC,mBAAmB,CAAC,CAAA;QACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;QACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;QAEhD,oDAAoD;QACpD,2CAA2C;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;QAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,SAAS;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;YACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,uBAAuB;oBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iBAC1B;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEJ,MAAM,UAAU,GAAG,SAAS;aACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;QAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;QAC/C,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;IACrC,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,OAAO,SAAS,CAAC,QAAQ,CAAA;IAC3B,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,OAAe;QACzB,IAAI,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YAC3B,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,OAAO,CAA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package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,4 +1,5 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
 export interface Mismatch {
     qual?: number;
@@ -13,28 +14,28 @@ export interface Mismatch {
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
-    constructor(record: any, _store: CramAdapter);
-    _get_name(): any;
+    constructor(record: CramRecord, _store: CramAdapter);
+    _get_name(): string | undefined;
     _get_start(): number;
     _get_end(): number;
-    _get_cram_read_features(): any;
+    _get_cram_read_features(): import("@gmod/cram/dist/cramFile/record").ReadFeature[] | undefined;
     _get_type(): string;
-    _get_score(): any;
-    _get_flags(): any;
+    _get_score(): number | undefined;
+    _get_flags(): number;
     _get_strand(): 1 | -1;
-    _read_group_id(): number | undefined;
-    _get_qual(): any;
-    qualRaw(): any;
+    _read_group_id(): string | undefined;
+    _get_qual(): string;
+    qualRaw(): number[] | null | undefined;
     _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
-    _get_pair_orientation(): any;
-    _get_template_length(): any;
+    _get_pair_orientation(): string | null | undefined;
+    _get_template_length(): number | undefined;
     _get_next_seq_id(): string | undefined;
-    _get_next_pos(): any;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
-    _get_tags(): any;
-    _get_seq(): any;
+    _get_tags(): Record<string, string>;
+    _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;