@jbrowse/plugin-alignments 2.16.0 → 2.17.0

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -30,7 +30,7 @@ const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const clone_1 = __importDefault(require("clone"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 // locals
 const util_1 = require("./util");
 const tagInfo_1 = require("./tagInfo");
@@ -41,7 +41,6 @@ const Formatter_1 = __importDefault(require("./Formatter"));
 // lazies
 const SupplementaryAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SupplementaryAlignments'))));
 const LinkedPairedAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinkedPairedAlignments'))));
-const omit = ['clipPos', 'flags'];
 const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureData } = model;
@@ -49,7 +48,7 @@ const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const SA = (0, util_1.getTag)('SA', feat);
     const { flags } = feat;
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, 
+        react_1.default.createElement(FeatureDetails_1.default, { ...props, 
             // @ts-expect-error
             descriptions: { ...tagInfo_1.tags, tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
         SA !== undefined ? (react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,

package/dist/AlignmentsFeatureDetail/Flags.js

@@ -7,7 +7,7 @@ exports.default = AlignmentFlags;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
@@ -34,7 +34,7 @@ function AlignmentFlags(props) {
     const { classes } = useStyles();
     const { feature } = props;
     const { flags } = feature;
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Flags" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Flags" },
         react_1.default.createElement(SimpleField_1.default, { name: "Flag", value: flags }),
         react_1.default.createElement(material_1.FormGroup, null, flagNames.map((name, idx) => {
             const val = flags & (1 << idx);

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SuppAlignments;
 const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const util_1 = require("@jbrowse/core/util");
 const LaunchPairedEndBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchPairedEndBreakpointSplitViewPanel"));
 function SuppAlignments(props) {
@@ -19,5 +19,5 @@ function SuppAlignments(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignments;
 const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
 const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
 function SupplementaryAlignments(props) {
@@ -20,7 +20,7 @@ function SupplementaryAlignments(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" },
         react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
         viewType ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -4,12 +4,12 @@ exports.getSAFeatures = getSAFeatures;
 const util_1 = require("@jbrowse/core/util");
 // locals
 const MismatchParser_1 = require("../MismatchParser");
-const util_2 = require("../util");
 async function getSAFeatures({ view, feature, }) {
+    var _a;
     const { assemblyManager } = (0, util_1.getSession)(view);
     const cigar = feature.get('CIGAR');
     const origStrand = feature.get('strand');
-    const SA = (0, util_2.getTag)(feature, 'SA') || '';
+    const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
     const readName = feature.get('name');
     const clipPos = (0, MismatchParser_1.getClip)(cigar, 1);
     // get the canonical refname for the read because if the read.get('refName')

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -92,8 +92,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -2,7 +2,7 @@ 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';
-import { IFilter } from '../shared';
+import { FilterBy } from '../shared/types';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -10,6 +10,7 @@ interface Header {
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
+    private ultraLongFeatureCache;
     private configureP?;
     protected configurePre(): Promise<{
         bam: BamFile;
@@ -30,7 +31,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: IFilter;
+        filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;

package/dist/BamAdapter/BamAdapter.js

@@ -4,15 +4,27 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bam_1 = require("@gmod/bam");
+const operators_1 = require("rxjs/operators");
+const rxjs_1 = require("rxjs");
+// jbrowse
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const operators_1 = require("rxjs/operators");
-const rxjs_2 = require("rxjs");
+const rxjs_2 = require("@jbrowse/core/util/rxjs");
+const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
 // locals
 const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
 class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        // used for avoiding re-creation new BamSlightlyLazyFeatures, keeping
+        // mismatches in cache. at an average of 100kb-300kb, keeping even just 500
+        // of these in memory is memory intensive but can reduce recomputation on
+        // these objects
+        this.ultraLongFeatureCache = new QuickLRU_1.default({
+            maxSize: 500,
+        });
+    }
     // derived classes may not use the same configuration so a custom configure
     // method allows derived classes to override this behavior
     async configurePre() {
@@ -100,7 +112,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             end,
             assemblyName: '',
         });
-        const seqChunks = await (0, rxjs_2.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
+        const seqChunks = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
         let sequence = '';
         seqChunks
             .sort((a, b) => a.get('start') - b.get('start'))
@@ -121,7 +133,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts) {
         const { refName, start, end, originalRefName } = region;
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+        return (0, rxjs_2.ObservableCreate)(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
             const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
@@ -129,26 +141,37 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
                 for (const record of records) {
                     let ref;
-                    if (!record.get('MD')) {
-                        ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
+                    if (!record.tags.MD) {
+                        ref = await this.seqFetch(originalRefName || refName, record.start, record.end);
                     }
                     const flags = record.flags;
                     if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
                         continue;
                     }
                     if (tagFilter) {
-                        const readVal = record.get(tagFilter.tag);
+                        const readVal = record.tags[tagFilter.tag];
                         const filterVal = tagFilter.value;
                         if (filterVal === '*'
-                            ? readVal !== undefined
+                            ? readVal === undefined
                             : `${readVal}` !== `${filterVal}`) {
                             continue;
                         }
                     }
-                    if (readName && record.get('name') !== readName) {
+                    if (readName && record.name !== readName) {
                         continue;
                     }
-                    observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
+                    // retrieve a feature from our feature cache if it is available, the
+                    // features in the cache have pre-computed mismatches objects that
+                    // can be re-used across blocks
+                    const ret = this.ultraLongFeatureCache.get(`${record.id}`);
+                    if (!ret) {
+                        const elt = new BamSlightlyLazyFeature_1.default(record, this, ref);
+                        this.ultraLongFeatureCache.set(`${record.id}`, elt);
+                        observer.next(elt);
+                    }
+                    else {
+                        observer.next(ret);
+                    }
                 }
                 observer.complete();
             });

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -6,26 +6,12 @@ export default class BamSlightlyLazyFeature implements Feature {
     private adapter;
     private ref?;
     constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
-    _get_name(): any;
-    _get_type(): string;
-    _get_score(): number;
-    _get_flags(): string;
-    _get_strand(): number;
-    _get_pair_orientation(): string | undefined;
-    _get_next_ref(): string | undefined;
-    _get_next_pos(): number | undefined;
-    _get_next_segment_position(): string | undefined;
-    _get_seq(): string;
-    qualRaw(): Buffer | undefined;
-    set(): void;
-    tags(): string[];
     id(): string;
+    get mismatches(): import("../shared/types").Mismatch[];
+    get qual(): string | undefined;
     get(field: string): any;
-    _get_refName(): string | undefined;
     parent(): undefined;
     children(): undefined;
-    pairedFeature(): boolean;
+    get fields(): SimpleFeatureSerialized;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("../MismatchParser").Mismatch[];
-    _get_clipPos(): number;
 }

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -2,6 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 // locals
 const MismatchParser_1 = require("../MismatchParser");
+const util_1 = require("../shared/util");
 class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -10,69 +11,22 @@ class BamSlightlyLazyFeature {
         this.adapter = adapter;
         this.ref = ref;
     }
-    _get_name() {
-        return this.record.get('name');
-    }
-    _get_type() {
-        return 'match';
-    }
-    _get_score() {
-        return this.record.get('mq');
-    }
-    _get_flags() {
-        return this.record.flags;
-    }
-    _get_strand() {
-        return this.record.isReverseComplemented() ? -1 : 1;
-    }
-    _get_pair_orientation() {
-        return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    }
-    _get_next_ref() {
-        return this.record.isPaired()
-            ? this.adapter.refIdToName(this.record._next_refid())
-            : undefined;
-    }
-    _get_next_pos() {
-        return this.record.isPaired() ? this.record._next_pos() : undefined;
-    }
-    _get_next_segment_position() {
-        return this.record.isPaired()
-            ? `${this.adapter.refIdToName(this.record._next_refid())}:${this.record._next_pos() + 1}`
-            : undefined;
-    }
-    _get_seq() {
-        return this.record.getReadBases();
-    }
-    qualRaw() {
-        return this.record.qualRaw();
+    id() {
+        return `${this.adapter.id}-${this.record.id}`;
     }
-    set() { }
-    tags() {
-        const properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
-        return [
-            ...new Set(properties
-                .filter(prop => prop.startsWith('_get_') &&
-                prop !== '_get_mismatches' &&
-                prop !== '_get_tags')
-                .map(methodName => methodName.replace('_get_', ''))
-                .concat(this.record._tags())),
-        ];
+    get mismatches() {
+        return (0, MismatchParser_1.getMismatches)(this.record.CIGAR, this.record.tags.MD, this.record.seq, this.ref, this.record.qual);
     }
-    id() {
-        return `${this.adapter.id}-${this.record.id()}`;
+    get qual() {
+        var _a;
+        return (_a = this.record.qual) === null || _a === void 0 ? void 0 : _a.join(' ');
     }
     get(field) {
-        const methodName = `_get_${field}`;
-        // @ts-expect-error
-        if (this[methodName]) {
-            // @ts-expect-error
-            return this[methodName]();
-        }
-        return this.record.get(field);
-    }
-    _get_refName() {
-        return this.adapter.refIdToName(this.record.seq_id());
+        return field === 'mismatches'
+            ? this.mismatches
+            : field === 'qual'
+                ? this.qual
+                : this.fields[field];
     }
     parent() {
         return undefined;
@@ -80,23 +34,39 @@ class BamSlightlyLazyFeature {
     children() {
         return undefined;
     }
-    pairedFeature() {
-        return false;
-    }
-    toJSON() {
+    get fields() {
+        const r = this.record;
+        const a = this.adapter;
+        const p = r.isPaired();
         return {
-            ...Object.fromEntries(this.tags()
-                .map(t => [t, this.get(t)])
-                .filter(elt => elt[1] !== undefined)),
+            start: r.start,
+            name: r.name,
+            end: r.end,
+            score: r.score,
+            strand: r.strand,
+            template_length: r.template_length,
+            flags: r.flags,
+            tags: r.tags,
+            refName: a.refIdToName(r.ref_id),
+            CIGAR: r.CIGAR,
+            seq: r.seq,
+            type: 'match',
+            pair_orientation: r.pair_orientation,
+            next_ref: p ? a.refIdToName(r.next_refid) : undefined,
+            next_pos: p ? r.next_pos : undefined,
+            next_segment_position: p
+                ? `${a.refIdToName(r.next_refid)}:${r.next_pos + 1}`
+                : undefined,
             uniqueId: this.id(),
         };
     }
-    _get_mismatches() {
-        return (0, MismatchParser_1.getMismatches)(this.get('CIGAR'), this.get('MD'), this.get('seq'), this.ref, this.qualRaw());
-    }
-    _get_clipPos() {
-        const cigar = this.get('CIGAR') || '';
-        return (0, MismatchParser_1.getClip)(cigar, this.get('strand'));
+    toJSON() {
+        return {
+            ...this.fields,
+            qual: this.qual,
+        };
     }
 }
 exports.default = BamSlightlyLazyFeature;
+(0, util_1.cacheGetter)(BamSlightlyLazyFeature, 'fields');
+(0, util_1.cacheGetter)(BamSlightlyLazyFeature, 'mismatches');

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,8 +1,8 @@
 import { IndexedCramFile, CramRecord } from '@gmod/cram';
 import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
+import type { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-import { IFilter } from '../shared';
+import { FilterBy } from '../shared/types';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
@@ -12,6 +12,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
     private configureP?;
+    private ultraLongFeatureCache;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
     configurePre(): Promise<{
@@ -33,7 +34,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: IFilter;
+        filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;

package/dist/CramAdapter/CramAdapter.js

@@ -4,18 +4,27 @@ 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_1 = require("@jbrowse/core/util/rxjs");
-const operators_1 = require("rxjs/operators");
-const rxjs_2 = require("rxjs");
+const rxjs_2 = require("@jbrowse/core/util/rxjs");
+const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
 // locals
 const CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
 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 = [];
     }
@@ -62,7 +71,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         if (!refName) {
             throw new Error('unknown');
         }
-        const seqChunks = await (0, rxjs_2.firstValueFrom)(sequenceAdapter
+        const seqChunks = await (0, rxjs_1.firstValueFrom)(sequenceAdapter
             .getFeatures({
             refName,
             start,
@@ -155,7 +164,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts) {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+        return (0, rxjs_2.ObservableCreate)(async (observer) => {
             const { cram, samHeader } = await this.setup(opts);
             const refId = this.refNameToId(refName);
             if (refId === undefined) {
@@ -182,7 +191,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                             : record.tags[tagFilter.tag];
                         const filterVal = tagFilter.value;
                         if (filterVal === '*'
-                            ? readVal !== undefined
+                            ? readVal === undefined
                             : `${readVal}` !== `${filterVal}`) {
                             continue;
                         }
@@ -190,7 +199,15 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     if (readName && record.readName !== readName) {
                         continue;
                     }
-                    observer.next(this.cramRecordToFeature(record));
+                    const ret = this.ultraLongFeatureCache.get(`${record.uniqueId}`);
+                    if (!ret) {
+                        const elt = this.cramRecordToFeature(record);
+                        this.ultraLongFeatureCache.set(`${record.uniqueId}`, elt);
+                        observer.next(elt);
+                    }
+                    else {
+                        observer.next(ret);
+                    }
                 }
                 observer.complete();
             });

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,39 +1,33 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
     constructor(record: CramRecord, _store: CramAdapter);
-    _get_name(): string | undefined;
-    _get_start(): number;
-    _get_end(): number;
-    _get_cram_read_features(): import("@gmod/cram/dist/cramFile/record").ReadFeature[] | undefined;
-    _get_type(): string;
-    _get_score(): number | undefined;
-    _get_flags(): number;
-    _get_strand(): 1 | -1;
-    _read_group_id(): string | undefined;
-    _get_qual(): string;
-    qualRaw(): number[] | null | undefined;
-    _get_refName(): string | undefined;
-    _get_is_paired(): boolean;
-    _get_pair_orientation(): string | null | undefined;
-    _get_template_length(): number | undefined;
-    _get_next_ref(): string | undefined;
-    _get_next_segment_position(): string | undefined;
-    _get_next_pos(): number | undefined;
-    _get_tags(): Record<string, string>;
-    _get_seq(): string | null | undefined;
-    _get_CIGAR(): string;
-    tags(): string[];
+    get name(): string | undefined;
+    get start(): number;
+    get end(): number;
+    get score(): number | undefined;
+    get flags(): number;
+    get strand(): 1 | -1;
+    get qual(): string;
+    get qualRaw(): number[] | null | undefined;
+    get refName(): string;
+    get pair_orientation(): string | null | undefined;
+    get template_length(): number | undefined;
+    get next_ref(): string | undefined;
+    get next_segment_position(): string | undefined;
+    get is_paired(): boolean;
+    get next_pos(): number | undefined;
+    get tags(): Record<string, string>;
+    get seq(): string | null | undefined;
+    get CIGAR(): string;
     id(): string;
     get(field: string): any;
     parent(): undefined;
     children(): undefined;
-    set(): void;
-    pairedFeature(): boolean;
-    _get_clipPos(): any;
+    get mismatches(): import("../shared/types").Mismatch[];
+    get fields(): SimpleFeatureSerialized;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./util").Mismatch[];
 }