@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/esm/AlignmentsTrack/configSchemaF.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configSchemaFactory(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,5 +80,5 @@ export default function configSchemaFactory(pluginManager: PluginManager): impor
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/esm/AlignmentsTrack/index.js

@@ -1,6 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
-import configSchemaF from './configSchemaF';
+import configSchemaF from "./configSchemaF.js";
+import { stringifySAM } from "../saveTrackFormats/sam.js";
 export default function register(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
@@ -8,7 +9,18 @@ export default function register(pm) {
             name: 'AlignmentsTrack',
             displayName: 'Alignments track',
             configSchema,
-            stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema).views(() => ({
+                saveTrackFileFormatOptions() {
+                    return {
+                        sam: {
+                            name: 'SAM',
+                            extension: 'sam',
+                            callback: stringifySAM,
+                            helpText: 'Note: SAM format export is experimental and does not currently output optional tags. The output may not fully conform to the SAM specification and should be validated before use in production workflows.',
+                        },
+                    };
+                },
+            })),
         });
         const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay');
         track.addDisplayType(linearAlignmentsDisplay);

package/esm/BamAdapter/BamAdapter.d.ts

@@ -1,39 +1,29 @@
 import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { FilterBy } from '../shared/types';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BamSlightlyLazyFeature from './BamSlightlyLazyFeature.ts';
+import type { FilterBy } from '../shared/types.ts';
+import type { ParsedSamHeader } from '../shared/util.ts';
+import type { BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
-interface Header {
-    idToName: string[];
-    nameToId: Record<string, number>;
-}
 export default class BamAdapter extends BaseFeatureDataAdapter {
-    private samHeader?;
+    samHeader?: ParsedSamHeader;
     private setupP?;
-    private ultraLongFeatureCache;
-    private configureP?;
-    protected configurePre(): Promise<{
-        bam: BamFile;
-        sequenceAdapter: BaseFeatureDataAdapter;
-    } | {
-        bam: BamFile;
-        sequenceAdapter?: undefined;
-    }>;
-    protected configure(): Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter;
-    }>;
+    protected configureResult?: {
+        bam: BamFile<BamSlightlyLazyFeature>;
+    };
+    private sequenceAdapterP?;
+    protected configure(): {
+        bam: BamFile<BamSlightlyLazyFeature>;
+    };
+    getSequenceAdapter(): Promise<BaseSequenceAdapter | undefined>;
     getHeader(_opts?: BaseOptions): Promise<string | undefined>;
-    private setupPre;
-    setupPre2(opts?: BaseOptions): Promise<Header>;
-    setup(opts?: BaseOptions): Promise<Header>;
+    private setup;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    private seqFetch;
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: FilterBy;
+        filterBy?: FilterBy;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;
@@ -41,4 +31,3 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     refIdToName(refId: number): string | undefined;
 }
-export {};

package/esm/BamAdapter/BamAdapter.js

@@ -1,175 +1,135 @@
 import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
+import { updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
-import { firstValueFrom } from 'rxjs';
-import { toArray } from 'rxjs/operators';
-import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
-import { filterReadFlag, filterTagValue } from '../shared/util';
+import BamSlightlyLazyFeature from "./BamSlightlyLazyFeature.js";
+import { parseSamHeader } from "../shared/util.js";
 export default class BamAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.ultraLongFeatureCache = new QuickLRU({
-            maxSize: 500,
-        });
-    }
-    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 BamFile({
-            bamFilehandle: openLocation(bamLocation, pm),
-            csiFilehandle: csi ? openLocation(location, pm) : undefined,
-            baiFilehandle: !csi ? openLocation(location, pm) : undefined,
-            yieldThreadTime: Number.POSITIVE_INFINITY,
-        });
-        const adapterConfig = this.getConf('sequenceAdapter');
-        if (adapterConfig && this.getSubAdapter) {
-            const { dataAdapter } = await this.getSubAdapter(adapterConfig);
-            return {
-                bam,
-                sequenceAdapter: dataAdapter,
+    samHeader;
+    setupP;
+    configureResult;
+    sequenceAdapterP;
+    configure() {
+        if (!this.configureResult) {
+            const bamLocation = this.getConf('bamLocation');
+            const location = this.getConf(['index', 'location']);
+            const indexType = this.getConf(['index', 'indexType']);
+            const csi = indexType === 'CSI';
+            this.configureResult = {
+                bam: new BamFile({
+                    bamFilehandle: openLocation(bamLocation, this.pluginManager),
+                    csiFilehandle: csi
+                        ? openLocation(location, this.pluginManager)
+                        : undefined,
+                    baiFilehandle: !csi
+                        ? openLocation(location, this.pluginManager)
+                        : undefined,
+                    recordClass: BamSlightlyLazyFeature,
+                }),
             };
         }
-        return { bam };
+        return this.configureResult;
     }
-    async configure() {
-        if (!this.configureP) {
-            this.configureP = this.configurePre().catch((e) => {
-                this.configureP = undefined;
-                throw e;
-            });
+    async getSequenceAdapter() {
+        const config = this.sequenceAdapterConfig;
+        if (!config || !this.getSubAdapter) {
+            return undefined;
         }
-        return this.configureP;
+        this.sequenceAdapterP ??= this.getSubAdapter(config)
+            .then(r => {
+            const adapter = r.dataAdapter;
+            return 'getSequence' in adapter ? adapter : undefined;
+        })
+            .catch((e) => {
+            this.sequenceAdapterP = undefined;
+            throw e;
+        });
+        return this.sequenceAdapterP;
     }
     async getHeader(_opts) {
-        const { bam } = await this.configure();
+        const { bam } = this.configure();
         return bam.getHeaderText();
     }
-    async setupPre(_opts) {
-        const { bam } = await this.configure();
-        const samHeader = await bam.getHeader();
-        const idToName = [];
-        const nameToId = {};
-        if (samHeader) {
-            for (const [refId, sqLine] of samHeader
-                .filter(l => l.tag === 'SQ')
-                .entries()) {
-                const SN = sqLine.data.find(item => item.tag === 'SN');
-                if (SN) {
-                    const refName = SN.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
+    async setup(opts) {
+        const { statusCallback } = opts || {};
+        this.setupP ??= updateStatus('Downloading index', statusCallback, async () => {
+            try {
+                const { bam } = this.configure();
+                const rawHeader = await bam.getHeader();
+                this.samHeader = parseSamHeader(rawHeader ?? []);
+                return this.samHeader;
             }
-        }
-        this.samHeader = { idToName, nameToId };
-        return this.samHeader;
-    }
-    async setupPre2(opts) {
-        if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch((e) => {
+            catch (e) {
                 this.setupP = undefined;
+                this.configureResult = undefined;
                 throw e;
-            });
-        }
+            }
+        });
         return this.setupP;
     }
-    async setup(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return updateStatus('Downloading index', statusCallback, () => this.setupPre2(opts));
-    }
     async getRefNames(opts) {
         const { idToName } = await this.setup(opts);
         return idToName;
     }
-    async seqFetch(refName, start, end) {
-        const { sequenceAdapter } = await this.configure();
-        const refSeqStore = sequenceAdapter;
-        if (!refSeqStore) {
-            return undefined;
-        }
-        if (!refName) {
-            return undefined;
-        }
-        const features = refSeqStore.getFeatures({
-            refName,
-            start,
-            end,
-            assemblyName: '',
-        });
-        const seqChunks = await firstValueFrom(features.pipe(toArray()));
-        let sequence = '';
-        for (const chunk of seqChunks.sort((a, b) => a.get('start') - b.get('start'))) {
-            const chunkStart = chunk.get('start');
-            const chunkEnd = chunk.get('end');
-            const trimStart = Math.max(start - chunkStart, 0);
-            const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
-            const trimLength = trimEnd - trimStart;
-            const chunkSeq = chunk.get('seq') || chunk.get('residues');
-            sequence += chunkSeq.slice(trimStart, trimStart + trimLength);
-        }
-        if (sequence.length !== end - start) {
-            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
-        }
-        return sequence;
-    }
     getFeatures(region, opts) {
         const { refName, start, end, originalRefName } = region;
         const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
-            const { bam } = await this.configure();
+            const { bam } = this.configure();
+            const sequenceAdapter = await this.getSequenceAdapter();
             await this.setup(opts);
             checkStopToken(stopToken);
-            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end));
+            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, { filterBy }));
             checkStopToken(stopToken);
             await updateStatus('Processing alignments', statusCallback, async () => {
-                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-                for (const record of records) {
-                    let ref;
-                    if (!record.tags.MD) {
-                        ref = await this.seqFetch(originalRefName || refName, record.start, record.end);
+                const { readName } = filterBy || {};
+                let regionSeq;
+                let regionStart = Infinity;
+                let regionEnd = 0;
+                if (sequenceAdapter) {
+                    for (const record of records) {
+                        if (!record.NUMERIC_MD) {
+                            regionStart = Math.min(regionStart, record.start);
+                            regionEnd = Math.max(regionEnd, record.end);
+                        }
                     }
-                    if (filterReadFlag(record.flags, flagInclude, flagExclude)) {
-                        continue;
-                    }
-                    if (tagFilter &&
-                        filterTagValue(record.tags[tagFilter.tag], tagFilter.value)) {
-                        continue;
+                    if (regionEnd > 0) {
+                        regionSeq = await sequenceAdapter.getSequence({
+                            refName: originalRefName || refName,
+                            start: regionStart,
+                            end: regionEnd,
+                        });
                     }
+                }
+                for (const record of records) {
                     if (readName && record.name !== readName) {
                         continue;
                     }
-                    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);
+                    record.adapter = this;
+                    if (!record.NUMERIC_MD && regionSeq) {
+                        record.ref = regionSeq.slice(record.start - regionStart, record.end - regionStart);
                     }
+                    observer.next(record);
                 }
                 observer.complete();
             });
         });
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
-        const { bam } = await this.configure();
+        const { bam } = this.configure();
         if (bam.index) {
-            const bytes = await bytesForRegions(regions, bam);
+            const bytes = await bam.estimatedBytesForRegions(regions);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
-            return { bytes, fetchSizeLimit };
+            return {
+                bytes,
+                fetchSizeLimit,
+            };
         }
         return super.getMultiRegionFeatureDensityStats(regions, opts);
     }
     refIdToName(refId) {
-        var _a;
-        return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];
+        return this.samHeader?.idToName[refId];
     }
 }

package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,17 +1,24 @@
-import type BamAdapter from './BamAdapter';
-import type { BamRecord } from '@gmod/bam';
-import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-export default class BamSlightlyLazyFeature implements Feature {
-    private record;
-    private adapter;
-    private ref?;
-    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
+import { BamRecord } from '@gmod/bam';
+import type BamAdapter from './BamAdapter.ts';
+import type { MismatchCallback } from '../shared/forEachMismatchTypes.ts';
+import type { Mismatch } from '../shared/types.ts';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default class BamSlightlyLazyFeature extends BamRecord implements Feature {
+    adapter: BamAdapter;
+    ref?: string;
+    private _cachedFields?;
     id(): string;
-    get mismatches(): import("../shared/types").Mismatch[];
-    get qual(): string | undefined;
+    get seq(): string;
+    get mismatches(): Mismatch[];
+    forEachMismatch(callback: MismatchCallback): void;
+    get qualString(): string | undefined;
+    get clipLengthAtStartOfRead(): number;
+    get refName(): string;
     get(field: string): any;
     parent(): undefined;
     children(): undefined;
     get fields(): SimpleFeatureSerialized;
+    get next_ref(): string | undefined;
+    get next_segment_position(): string | undefined;
     toJSON(): SimpleFeatureSerialized;
 }