@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -32,15 +32,16 @@ const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const clone_1 = __importDefault(require("clone"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const MismatchParser_1 = require("../BamAdapter/MismatchParser");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
+const useStyles = (0, mui_1.makeStyles)()({
     compact: {
         paddingRight: 0,
         paddingTop: 0,
         paddingBottom: 0,
     },
-}));
+});
 const omit = ['clipPos', 'flags'];
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFlags(props) {
@@ -120,12 +121,12 @@ function SupplementaryAlignments(props) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`;
             return (react_1.default.createElement("li", { key: `${locString}-${index}` },
-                react_1.default.createElement(material_1.Link, { onClick: event => {
+                react_1.default.createElement(material_1.Link, { onClick: async (event) => {
                         event.preventDefault();
                         const { view } = model;
                         try {
                             if (view) {
-                                view.navToLocString(locString);
+                                await view.navToLocString(locString);
                             }
                             else {
                                 throw new Error('No view associated with this view anymore');
@@ -141,15 +142,13 @@ function SupplementaryAlignments(props) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function PairLink({ locString, model }) {
     const session = (0, util_1.getSession)(model);
-    return (react_1.default.createElement(material_1.Link, { onClick: () => {
+    return (react_1.default.createElement(material_1.Link, { onClick: async () => {
             const { view } = model;
+            if (!view) {
+                throw new Error('No view associated with this feature detail panel anymore');
+            }
             try {
-                if (view) {
-                    view.navToLocString(locString);
-                }
-                else {
-                    session.notify('No view associated with this feature detail panel anymore', 'warning');
-                }
+                await view.navToLocString(locString);
             }
             catch (e) {
                 console.error(e);
@@ -160,14 +159,14 @@ function PairLink({ locString, model }) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFeatureDetails(props) {
     const { model } = props;
-    const feat = JSON.parse(JSON.stringify(model.featureData));
+    const feat = (0, clone_1.default)(model.featureData);
     const SA = (feat.tags && feat.tags.SA) || feat.SA;
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
         react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, feature: feat, formatter: (value, key) => {
                 return key === 'next_segment_position' ? (react_1.default.createElement(PairLink, { model: model, locString: value })) : (react_1.default.createElement(Formatter, { value: value }));
             } }),
         SA ? react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
-        react_1.default.createElement(AlignmentFlags, { feature: feat, ...props })));
+        feat.flags !== undefined ? (react_1.default.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
 }
 exports.default = (0, mobx_react_1.observer)(AlignmentFeatureDetails);
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
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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

@@ -1,7 +1,7 @@
 import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -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 +9,48 @@ 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");
+// locals
 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 +166,7 @@ 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/BamSlightlyLazyFeature.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+// locals
 const MismatchParser_1 = require("./MismatchParser");
 class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class

package/dist/BamAdapter/BamSlightlyLazyFeature.js.map

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

@@ -10,13 +10,13 @@ export interface Mismatch {
     cliplen?: number;
 }
 export declare function parseCigar(cigar?: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference
  * @returns array of mismatches and their positions
  */
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): {
     type: string;

package/dist/BamAdapter/MismatchParser.js

@@ -60,7 +60,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
             });
         }
         else if (op === 'X') {
-            const r = seq.slice(soffset, soffset + len);
+            const r = (seq === null || seq === void 0 ? void 0 : seq.slice(soffset, soffset + len)) || [];
             const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
             for (let j = 0; j < len; j++) {
                 mismatches.push({
@@ -172,10 +172,7 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
                 }
                 const s = getTemplateCoordLocal(curr.start);
                 curr.base = seq[s] || 'X';
-                const qualScore = qual === null || qual === void 0 ? void 0 : qual[s];
-                if (qualScore) {
-                    curr.qual = qualScore;
-                }
+                curr.qual = qual === null || qual === void 0 ? void 0 : qual[s];
                 curr.altbase = token;
                 nextRecord();
             }
@@ -192,7 +189,7 @@ function getMismatches(cigar, md, seq, ref, qual) {
         mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual));
     }
     // now let's look for CRAM or MD mismatches
-    if (md) {
+    if (md && seq) {
         mismatches = mismatches.concat(mdToMismatches(md, ops, mismatches, seq, qual));
     }
     return mismatches;
@@ -291,7 +288,7 @@ function getModificationTypes(mm) {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
-            throw new Error('bad format for MM tag');
+            throw new Error(`bad format for MM tag: ${mm}`);
         }
         const [, , , typestr] = matches;
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so

package/dist/BamAdapter/MismatchParser.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: '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',
         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,uGAAuG;QACzG,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/BamAdapter/index.js

@@ -29,10 +29,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BamAdapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'BamAdapter',
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/dist/BamAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,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;
     }>;
     /**