@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,76 +1,27 @@
-// 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
     constructor(record, adapter, ref) {
         this.record = record;
         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_${field}`;
-        // @ts-expect-error
-        if (this[methodName]) {
-            // @ts-expect-error
-            return this[methodName]();
-        }
-        return this.record.get(field);
-    }
-    _get_refName() {
-        return this.adapter.refIdToName(this.record.seq_id());
+        return field === 'mismatches'
+            ? this.mismatches
+            : field === 'qual'
+                ? this.qual
+                : this.fields[field];
     }
     parent() {
         return undefined;
@@ -78,22 +29,38 @@ export default class BamSlightlyLazyFeature {
     children() {
         return undefined;
     }
-    pairedFeature() {
-        return false;
-    }
-    toJSON() {
+    get fields() {
+        const r = this.record;
+        const a = this.adapter;
+        const p = r.isPaired();
         return {
-            ...Object.fromEntries(this.tags()
-                .map(t => [t, this.get(t)])
-                .filter(elt => elt[1] !== undefined)),
+            start: r.start,
+            name: r.name,
+            end: r.end,
+            score: r.score,
+            strand: r.strand,
+            template_length: r.template_length,
+            flags: r.flags,
+            tags: r.tags,
+            refName: a.refIdToName(r.ref_id),
+            CIGAR: r.CIGAR,
+            seq: r.seq,
+            type: 'match',
+            pair_orientation: r.pair_orientation,
+            next_ref: p ? a.refIdToName(r.next_refid) : undefined,
+            next_pos: p ? r.next_pos : undefined,
+            next_segment_position: p
+                ? `${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/BamAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bamLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,19 +20,11 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     fetchSizeLimit: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: string;
         description: string;

package/esm/BamAdapter/configSchema.js

@@ -1,30 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config BamAdapter
- * used to configure BAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('BamAdapter', {
-    /**
-     * #slot
-     */
     bamLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('BamIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['BAI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'BAI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -33,19 +20,11 @@ const configSchema = ConfigurationSchema('BamAdapter', {
             },
         },
     }),
-    /**
-     * #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',

package/esm/BamAdapter/index.d.ts

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

package/esm/CramAdapter/CramAdapter.d.ts

@@ -1,8 +1,10 @@
-import { IndexedCramFile, CramRecord } from '@gmod/cram';
-import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
+import { IndexedCramFile } from '@gmod/cram';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-import { IFilter } from '../shared';
+import type { FilterBy } from '../shared/types';
+import type { CramRecord } from '@gmod/cram';
+import type { BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
@@ -12,6 +14,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
     private configureP?;
+    private ultraLongFeatureCache;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
     configurePre(): Promise<{
@@ -33,7 +36,7 @@ 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;
@@ -41,11 +44,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         bytes: number;
         fetchSizeLimit: any;
     }>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
     private bytesForRegions;
 }
 export {};

package/esm/CramAdapter/CramAdapter.js

@@ -1,17 +1,21 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal, updateStatus, toLocale, } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { toLocale, updateStatus } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { toArray } from 'rxjs/operators';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom } from 'rxjs';
-// locals
+import { toArray } from 'rxjs/operators';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+import { filterReadFlag, filterTagValue } from '../shared/util';
 export default class CramAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.samHeader = {};
-        // maps a seqId to original refname, passed specially to render args, to a seqid
+        this.ultraLongFeatureCache = new QuickLRU({
+            maxSize: 500,
+        });
         this.seqIdToOriginalRefName = [];
     }
     async configurePre() {
@@ -51,7 +55,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return cram.cram.getHeaderText();
     }
     async seqFetch(seqId, start, end) {
-        start -= 1; // convert from 1-based closed to interbase
+        start -= 1;
         const { sequenceAdapter } = await this.configure();
         const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
         if (!refName) {
@@ -89,8 +93,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             const conf = await this.configure();
             const { cram } = conf;
             const samHeader = await cram.cram.getSamHeader();
-            // use the @SQ lines in the header to figure out the
-            // mapping between ref ID numbers and names
             const idToName = [];
             const nameToId = {};
             samHeader
@@ -127,8 +129,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         return samHeader.idToName;
     }
-    // use info from the SAM header if possible, but fall back to using
-    // the ref seq order from when the browser's refseqs were loaded
     refNameToId(refName) {
         if (this.samHeader.nameToId) {
             return this.samHeader.nameToId[refName];
@@ -138,8 +138,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         return undefined;
     }
-    // use info from the SAM header if possible, but fall back to using
-    // the ref seq order from when the browser's refseqs were loaded
     refIdToName(refId) {
         var _a, _b;
         return ((_a = this.samHeader.idToName) === null || _a === void 0 ? void 0 : _a[refId]) || ((_b = this.seqIdToRefName) === null || _b === void 0 ? void 0 : _b[refId]);
@@ -148,7 +146,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return this.seqIdToOriginalRefName[refId];
     }
     getFeatures(region, opts) {
-        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return ObservableCreate(async (observer) => {
             const { cram, samHeader } = await this.setup(opts);
@@ -162,40 +160,41 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
             const records = await updateStatus('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
-            checkAbortSignal(signal);
+            checkStopToken(stopToken);
             await updateStatus('Processing alignments', statusCallback, () => {
                 var _a;
                 const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
                 for (const record of records) {
-                    const flags = record.flags;
-                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                    if (filterReadFlag(record.flags, flagInclude, flagExclude)) {
                         continue;
                     }
-                    if (tagFilter) {
-                        const readVal = tagFilter.tag === 'RG'
+                    if (tagFilter &&
+                        filterTagValue(tagFilter.tag === 'RG'
                             ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
-                            : record.tags[tagFilter.tag];
-                        const filterVal = tagFilter.value;
-                        if (filterVal === '*'
-                            ? readVal !== undefined
-                            : `${readVal}` !== `${filterVal}`) {
-                            continue;
-                        }
+                            : record.tags[tagFilter.tag], tagFilter.value)) {
+                        continue;
                     }
                     if (readName && record.readName !== readName) {
                         continue;
                     }
-                    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();
             });
-        }, signal);
+        }, stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
     cramRecordToFeature(record) {
         return new CramSlightlyLazyFeature(record, this);
     }
-    // we return the configured fetchSizeLimit, and the bytes for the region
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
@@ -204,11 +203,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             fetchSizeLimit,
         };
     }
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
     async bytesForRegions(regions, _opts) {
         const { cram } = await this.configure();
         const blockResults = await Promise.all(regions.map(region => {

package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,39 +1,33 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { CramRecord } from '@gmod/cram';
-import CramAdapter from './CramAdapter';
+import type CramAdapter from './CramAdapter';
+import type { CramRecord } from '@gmod/cram';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
     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[];
 }