@jbrowse/plugin-alignments 2.16.1 → 2.17.0

package/dist/shared/util.js

@@ -1,6 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.defaultFilterFlags = void 0;
 exports.hasPairedReads = hasPairedReads;
+exports.alphaColor = alphaColor;
+exports.cacheGetter = cacheGetter;
+const colord_1 = require("@jbrowse/core/util/colord");
 function hasPairedReads(features) {
     for (const f of features.chains.values()) {
         if (f[0].flags & 1) {
@@ -9,3 +13,25 @@ function hasPairedReads(features) {
     }
     return false;
 }
+function alphaColor(baseColor, p) {
+    return p !== 1
+        ? (0, colord_1.colord)(baseColor)
+            .alpha(p * p)
+            .toHslString()
+        : baseColor;
+}
+exports.defaultFilterFlags = {
+    flagInclude: 0,
+    flagExclude: 1540,
+};
+function cacheGetter(ctor, prop) {
+    const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
+    const getter = desc.get;
+    Object.defineProperty(ctor.prototype, prop, {
+        get() {
+            const ret = getter.call(this);
+            Object.defineProperty(this, prop, { value: ret });
+            return ret;
+        },
+    });
+}

package/dist/util.d.ts

@@ -2,7 +2,6 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { Feature, AugmentedRegion } from '@jbrowse/core/util';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { IAutorunOptions } from 'mobx';
-export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
     fr: Record<string, string>;
@@ -17,11 +16,15 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
-export declare const modificationColors: Record<string, string>;
+interface ModificationData {
+    color: string;
+    name: string;
+}
+export declare const modificationData: Record<string, ModificationData>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
 export declare function randomColor(str: string): string;
+export declare function getColorForModification(str: string): string;
 export {};

package/dist/util.js

@@ -1,28 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTag = getTag;
+exports.modificationData = exports.pairMap = exports.orientationTypes = void 0;
 exports.getTagAlt = getTagAlt;
 exports.getColorWGBS = getColorWGBS;
 exports.fetchSequence = fetchSequence;
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
 exports.createAutorun = createAutorun;
 exports.randomColor = randomColor;
+exports.getColorForModification = getColorForModification;
 const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
-function getTag(feature, tag) {
-    const tags = feature.get('tags');
-    return tags !== undefined ? tags[tag] : feature.get(tag);
-}
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
     var _a;
-    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
+    const tags = feature.get('tags');
+    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
 }
 // orientation definitions from igv.js, see also
 // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
@@ -83,8 +77,6 @@ function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -92,28 +84,27 @@ async function fetchSequence(region, adapter) {
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
+        end,
+        start,
     })
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// has to check underlying C-G (aka CpG) on the reference sequence
-function shouldFetchReferenceSequence(type) {
-    return type === 'methylation';
-}
 // adapted from IGV
-// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
-exports.modificationColors = {
-    m: 'rgb(255,0,0)',
-    h: 'rgb(11, 132, 165)',
-    o: 'rgb(111, 78, 129)',
-    f: 'rgb(246, 200, 95)',
-    c: 'rgb(157, 216, 102)',
-    g: 'rgb(255, 160, 86)',
-    e: 'rgb(141, 221, 208)',
-    b: 'rgb(202, 71, 47)',
-    a: 'hsl(136, 50%, 50%)',
+// https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/resources/org/broad/igv/prefs/preferences.tab#L230-L242
+exports.modificationData = {
+    m: { color: 'rgb(255,0,0)', name: '5mC' },
+    h: { color: 'rgb(255,0,255)', name: '5hmC' },
+    o: { color: 'rgb(111, 78, 129)', name: '8oxoG' },
+    f: { color: 'rgb(246, 200, 95)', name: '5fC' },
+    c: { color: 'rgb(157, 216, 102)', name: '5cac' },
+    g: { color: 'rgb(255, 160, 86)', name: '5hmu' },
+    e: { color: 'rgb(141, 221, 208)', name: '5fU' },
+    b: { color: 'rgb(0,100,47)', name: '5caU' },
+    a: { color: 'rgb(51,0,111)', name: '6mA' },
+    17082: { color: 'rgb(51,153,255)', name: 'pseU' },
+    17596: { color: 'rgb(102,153,0)', name: 'inosine' },
+    21839: { color: 'rgb(153,0,153)', name: '4mC' },
 };
 function createAutorun(self, cb, opts) {
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
@@ -134,3 +125,7 @@ function randomColor(str) {
     }
     return `hsl(${sum * 10}, 20%, 50%)`;
 }
+function getColorForModification(str) {
+    var _a;
+    return ((_a = exports.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -13,7 +13,6 @@ import Formatter from './Formatter';
 // lazies
 const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'));
 const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'));
-const omit = ['clipPos', 'flags'];
 const AlignmentsFeatureDetails = observer(function (props) {
     const { model } = props;
     const { featureData } = model;
@@ -21,7 +20,7 @@ const AlignmentsFeatureDetails = observer(function (props) {
     const SA = getTag('SA', feat);
     const { flags } = feat;
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
-        React.createElement(FeatureDetails, { ...props, omit: omit, 
+        React.createElement(FeatureDetails, { ...props, 
             // @ts-expect-error
             descriptions: { ...tags, tags: tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
         SA !== undefined ? (React.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,

package/esm/AlignmentsFeatureDetail/getSAFeatures.js

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

package/esm/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/esm/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/esm/BamAdapter/BamAdapter.js

@@ -1,13 +1,25 @@
 import { BamFile } from '@gmod/bam';
+import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
+// jbrowse
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 // locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
 export default class BamAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        // used for avoiding re-creation new BamSlightlyLazyFeatures, keeping
+        // mismatches in cache. at an average of 100kb-300kb, keeping even just 500
+        // of these in memory is memory intensive but can reduce recomputation on
+        // these objects
+        this.ultraLongFeatureCache = new QuickLRU({
+            maxSize: 500,
+        });
+    }
     // derived classes may not use the same configuration so a custom configure
     // method allows derived classes to override this behavior
     async configurePre() {
@@ -124,26 +136,37 @@ export default class BamAdapter extends 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(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(`${record.id}`);
+                    if (!ret) {
+                        const elt = new BamSlightlyLazyFeature(record, this, ref);
+                        this.ultraLongFeatureCache.set(`${record.id}`, elt);
+                        observer.next(elt);
+                    }
+                    else {
+                        observer.next(ret);
+                    }
                 }
                 observer.complete();
             });

package/esm/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/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,5 +1,6 @@
 // locals
-import { getClip, getMismatches } from '../MismatchParser';
+import { getMismatches } from '../MismatchParser';
+import { cacheGetter } from '../shared/util';
 export default class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -8,69 +9,22 @@ export default 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 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_${field}`;
-        // @ts-expect-error
-        if (this[methodName]) {
-            // @ts-expect-error
-            return this[methodName]();
-        }
-        return this.record.get(field);
-    }
-    _get_refName() {
-        return this.adapter.refIdToName(this.record.seq_id());
+        return field === 'mismatches'
+            ? this.mismatches
+            : field === 'qual'
+                ? this.qual
+                : this.fields[field];
     }
     parent() {
         return undefined;
@@ -78,22 +32,38 @@ export default class BamSlightlyLazyFeature {
     children() {
         return undefined;
     }
-    pairedFeature() {
-        return false;
-    }
-    toJSON() {
+    get fields() {
+        const r = this.record;
+        const a = this.adapter;
+        const p = r.isPaired();
         return {
-            ...Object.fromEntries(this.tags()
-                .map(t => [t, this.get(t)])
-                .filter(elt => elt[1] !== undefined)),
+            start: r.start,
+            name: r.name,
+            end: r.end,
+            score: r.score,
+            strand: r.strand,
+            template_length: r.template_length,
+            flags: r.flags,
+            tags: r.tags,
+            refName: a.refIdToName(r.ref_id),
+            CIGAR: r.CIGAR,
+            seq: r.seq,
+            type: 'match',
+            pair_orientation: r.pair_orientation,
+            next_ref: p ? a.refIdToName(r.next_refid) : undefined,
+            next_pos: p ? r.next_pos : undefined,
+            next_segment_position: p
+                ? `${a.refIdToName(r.next_refid)}:${r.next_pos + 1}`
+                : undefined,
             uniqueId: this.id(),
         };
     }
-    _get_mismatches() {
-        return getMismatches(this.get('CIGAR'), this.get('MD'), this.get('seq'), this.ref, this.qualRaw());
-    }
-    _get_clipPos() {
-        const cigar = this.get('CIGAR') || '';
-        return getClip(cigar, this.get('strand'));
+    toJSON() {
+        return {
+            ...this.fields,
+            qual: this.qual,
+        };
     }
 }
+cacheGetter(BamSlightlyLazyFeature, 'fields');
+cacheGetter(BamSlightlyLazyFeature, 'mismatches');

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

@@ -1,16 +1,25 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
+import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
+// jbrowse
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal, updateStatus, toLocale, } from '@jbrowse/core/util';
+import { checkAbortSignal, updateStatus, toLocale } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 // locals
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
 export default class CramAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.samHeader = {};
+        // used for avoiding re-creation new BamSlightlyLazyFeatures, keeping
+        // mismatches in cache. at an average of 100kb-300kb, keeping even just 500
+        // of these in memory is fairly intensive but can reduce recomputation on
+        // these objects
+        this.ultraLongFeatureCache = new QuickLRU({
+            maxSize: 500,
+        });
         // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
@@ -177,7 +186,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                             : record.tags[tagFilter.tag];
                         const filterVal = tagFilter.value;
                         if (filterVal === '*'
-                            ? readVal !== undefined
+                            ? readVal === undefined
                             : `${readVal}` !== `${filterVal}`) {
                             continue;
                         }
@@ -185,7 +194,15 @@ export default class CramAdapter extends 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/esm/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[];
 }