@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/BamAdapter/MismatchParser.js.map

@@ -0,0 +1 @@
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package/esm/BamAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/BamAdapter/configSchema.js

@@ -0,0 +1,31 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export default types.late(() => ConfigurationSchema('BamAdapter', {
+    bamLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+    },
+    index: ConfigurationSchema('BamIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['BAI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'BAI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.bam.bai',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    fetchSizeLimit: {
+        type: 'number',
+        defaultValue: 5000000,
+    },
+    sequenceAdapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true }));
+//# sourceMappingURL=configSchema.js.map

package/esm/BamAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BamAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CAC7B,mBAAmB,CACjB,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IACD,KAAK,EAAE,mBAAmB,CAAC,UAAU,EAAE;QACrC,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,qBAAqB;gBAC1B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;KACxB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}

package/esm/BamAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/BamAdapter/index.js

@@ -0,0 +1,10 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BamAdapter',
+        configSchema,
+        getAdapterClass: () => import('./BamAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/BamAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/CramAdapter/CramAdapter.d.ts

@@ -0,0 +1,53 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+interface Header {
+    idToName?: string[];
+    nameToId?: Record<string, number>;
+    readGroups?: number[];
+}
+interface FilterBy {
+    flagInclude: number;
+    flagExclude: number;
+    tagFilter: {
+        tag: string;
+        value: unknown;
+    };
+    readName: string;
+}
+export default class CramAdapter extends BaseFeatureDataAdapter {
+    samHeader: Header;
+    private setupP?;
+    private seqIdToRefName;
+    private seqIdToOriginalRefName;
+    configure(): Promise<{
+        cram: any;
+        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private seqFetch;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    refNameToId(refName: string): number | undefined;
+    refIdToName(refId: number): string | undefined;
+    refIdToOriginalName(refId: number): string;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: FilterBy;
+    }): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+        bytes: any;
+        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

@@ -0,0 +1,228 @@
+import { CraiIndex, IndexedCramFile } from '@gmod/cram';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { checkAbortSignal } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { toArray } from 'rxjs/operators';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+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.seqIdToOriginalRefName = [];
+    }
+    async configure() {
+        const cramLocation = this.getConf('cramLocation');
+        const craiLocation = this.getConf('craiLocation');
+        if (!cramLocation) {
+            throw new Error('missing cramLocation argument');
+        }
+        if (!craiLocation) {
+            throw new Error('missing craiLocation argument');
+        }
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const cram = new IndexedCramFile({
+            cramFilehandle: openLocation(cramLocation, this.pluginManager),
+            index: new CraiIndex({
+                filehandle: openLocation(craiLocation, this.pluginManager),
+            }),
+            seqFetch: this.seqFetch.bind(this),
+            checkSequenceMD5: false,
+            fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
+        });
+        // instantiate the sequence adapter
+        const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
+        if (!this.getSubAdapter) {
+            throw new Error('Error getting subadapter');
+        }
+        const seqConf = this.getConf('sequenceAdapter');
+        const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf);
+        if (!(sequenceAdapter instanceof BaseFeatureDataAdapter)) {
+            throw new Error(`CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`);
+        }
+        return { cram, sequenceAdapter };
+    }
+    async getHeader(opts) {
+        const { cram } = await this.configure();
+        return cram.cram.getHeaderText(opts);
+    }
+    async seqFetch(seqId, start, end) {
+        start -= 1; // convert from 1-based closed to interbase
+        const { sequenceAdapter } = await this.configure();
+        const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
+        if (!refName) {
+            return undefined;
+        }
+        const seqChunks = await sequenceAdapter
+            .getFeatures({
+            refName,
+            start,
+            end,
+            assemblyName: '',
+        })
+            .pipe(toArray())
+            .toPromise();
+        const sequence = seqChunks
+            .sort((a, b) => a.get('start') - b.get('start'))
+            .map(chunk => {
+            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');
+            return chunkSeq.substr(trimStart, trimLength);
+        })
+            .join('');
+        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;
+    }
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const configured = await this.configure();
+        statusCallback('Downloading index');
+        const { cram } = configured;
+        const samHeader = await cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+        // use the @SQ lines in the header to figure out the
+        // mapping between ref ID numbers and names
+        const idToName = [];
+        const nameToId = {};
+        samHeader
+            .filter(l => l.tag === 'SQ')
+            .forEach((sqLine, refId) => {
+            sqLine.data.forEach(item => {
+                if (item.tag === 'SN') {
+                    // this is the ref name
+                    const refName = item.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
+            });
+        });
+        const readGroups = samHeader
+            .filter(l => l.tag === 'RG')
+            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
+        const data = { idToName, nameToId, readGroups };
+        statusCallback('');
+        this.samHeader = data;
+        return { samHeader: data, ...configured };
+    }
+    async setup(opts) {
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async getRefNames(opts) {
+        const { samHeader } = await this.setup(opts);
+        if (!samHeader.idToName) {
+            throw new Error('CRAM file has no header lines');
+        }
+        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];
+        }
+        if (this.seqIdToRefName) {
+            return this.seqIdToRefName.indexOf(refName);
+        }
+        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) {
+        if (this.samHeader.idToName) {
+            return this.samHeader.idToName[refId];
+        }
+        if (this.seqIdToRefName) {
+            return this.seqIdToRefName[refId];
+        }
+        return undefined;
+    }
+    refIdToOriginalName(refId) {
+        return this.seqIdToOriginalRefName[refId];
+    }
+    getFeatures(region, opts) {
+        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { refName, start, end, originalRefName } = region;
+        return ObservableCreate(async (observer) => {
+            const { cram, sequenceAdapter } = await this.setup(opts);
+            statusCallback('Downloading alignments');
+            if (!this.seqIdToRefName) {
+                this.seqIdToRefName = await sequenceAdapter.getRefNames(opts);
+            }
+            const refId = this.refNameToId(refName);
+            if (refId !== undefined) {
+                if (originalRefName) {
+                    this.seqIdToOriginalRefName[refId] = originalRefName;
+                }
+                const records = await cram.getRecordsForRange(refId, start, end, opts);
+                checkAbortSignal(signal);
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                let filtered = records.filter((record) => {
+                    const flags = record.flags;
+                    return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
+                });
+                if (tagFilter) {
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    filtered = filtered.filter((record) => {
+                        const val = record[tagFilter.tag];
+                        return val === '*' ? val !== undefined : val === tagFilter.value;
+                    });
+                }
+                if (readName) {
+                    filtered = filtered.filter(
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    (record) => record.readName === readName);
+                }
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                filtered.forEach((record) => {
+                    observer.next(this.cramRecordToFeature(record));
+                });
+            }
+            else {
+                console.warn('Unknown refName', refName);
+            }
+            statusCallback('');
+            observer.complete();
+        }, signal);
+    }
+    freeResources( /* { region } */) { }
+    cramRecordToFeature(record) {
+        return new CramSlightlyLazyFeature(record, this);
+    }
+    // we return the configured fetchSizeLimit, and the bytes for the region
+    async estimateRegionsStats(regions, opts) {
+        const bytes = await this.bytesForRegions(regions, opts);
+        const fetchSizeLimit = this.getConf('fetchSizeLimit');
+        return {
+            bytes,
+            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 => {
+            const { refName, start, end } = region;
+            const chrId = this.refNameToId(refName);
+            return cram.index.getEntriesForRange(chrId, start, end);
+        }));
+        return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
+    }
+}
+//# sourceMappingURL=CramAdapter.js.map

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@@ -0,0 +1 @@
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package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -0,0 +1,49 @@
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import CramAdapter from './CramAdapter';
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export default class CramSlightlyLazyFeature implements Feature {
+    private record;
+    private _store;
+    constructor(record: any, _store: CramAdapter);
+    _get_name(): any;
+    _get_start(): number;
+    _get_end(): number;
+    _get_cram_read_features(): any;
+    _get_type(): string;
+    _get_score(): any;
+    _get_flags(): any;
+    _get_strand(): 1 | -1;
+    _read_group_id(): number | undefined;
+    _get_qual(): any;
+    qualRaw(): any;
+    _get_seq_id(): string | undefined;
+    _get_refName(): string | undefined;
+    _get_is_paired(): boolean;
+    _get_pair_orientation(): any;
+    _get_template_length(): any;
+    _get_next_seq_id(): string | undefined;
+    _get_next_pos(): any;
+    _get_next_segment_position(): string | undefined;
+    _get_tags(): any;
+    _get_seq(): any;
+    _get_CIGAR(): string;
+    tags(): string[];
+    id(): string;
+    get(field: string): any;
+    parent(): undefined | Feature;
+    children(): undefined | Feature[];
+    set(): void;
+    pairedFeature(): boolean;
+    _get_clipPos(): any;
+    toJSON(): SimpleFeatureSerialized;
+    _get_mismatches(): Mismatch[];
+}