@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/esm/BamAdapter/configSchema.js

@@ -1,16 +1,30 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-export default types.late(() => ConfigurationSchema('BamAdapter', {
+/**
+ * #config BamAdapter
+ * used to configure BAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+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: {
@@ -19,13 +33,24 @@ export default types.late(() => ConfigurationSchema('BamAdapter', {
             },
         },
     }),
+    /**
+     * #slot
+     */
     fetchSizeLimit: {
         type: 'number',
+        description: 'used to determine when 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',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/esm/BamAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"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;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IAED,KAAK,EAAE,mBAAmB,CAAC,UAAU,EAAE;QACrC;;WAEG;QACH,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;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,qBAAqB;gBAC1B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,4FAA4F;QAC9F,YAAY,EAAE,OAAS;KACxB;IACD;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/esm/CramAdapter/CramAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { IndexedCramFile, CramRecord } from '@gmod/cram';
+import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } 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[];
+    readGroups?: (string | undefined)[];
 }
 interface FilterBy {
     flagInclude: number;
@@ -18,13 +19,18 @@ interface FilterBy {
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
+    private configureP?;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
+    configurePre(): Promise<{
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
+    }>;
     configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -38,9 +44,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
+        bytes: number;
         fetchSizeLimit: any;
     }>;
     /**

package/esm/CramAdapter/CramAdapter.js

@@ -12,7 +12,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
-    async configure() {
+    async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
         if (!cramLocation) {
@@ -21,38 +21,43 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         if (!craiLocation) {
             throw new Error('missing craiLocation argument');
         }
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const pm = this.pluginManager;
         const cram = new IndexedCramFile({
-            cramFilehandle: openLocation(cramLocation, this.pluginManager),
-            index: new CraiIndex({
-                filehandle: openLocation(craiLocation, this.pluginManager),
-            }),
-            seqFetch: this.seqFetch.bind(this),
+            cramFilehandle: openLocation(cramLocation, pm),
+            index: new CraiIndex({ filehandle: openLocation(craiLocation, pm) }),
+            seqFetch: (...args) => this.seqFetch(...args),
             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}'`);
+        const subadapter = await this.getSubAdapter(seqConf);
+        return {
+            cram,
+            sequenceAdapter: subadapter.dataAdapter,
+        };
+    }
+    async configure() {
+        if (!this.configureP) {
+            this.configureP = this.configurePre().catch(e => {
+                this.configureP = undefined;
+                throw e;
+            });
         }
-        return { cram, sequenceAdapter };
+        return this.configureP;
     }
     async getHeader(opts) {
         const { cram } = await this.configure();
-        return cram.cram.getHeaderText(opts);
+        return cram.cram.getHeaderText();
     }
     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;
+            throw new Error('unknown');
         }
         const seqChunks = await sequenceAdapter
             .getFeatures({
@@ -82,10 +87,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const configured = await this.configure();
+        const conf = await this.configure();
         statusCallback('Downloading index');
-        const { cram } = configured;
-        const samHeader = await cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+        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 = [];
@@ -108,7 +113,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         const data = { idToName, nameToId, readGroups };
         statusCallback('');
         this.samHeader = data;
-        return { samHeader: data, ...configured };
+        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -140,13 +145,8 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     // 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;
+        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]);
     }
     refIdToOriginalName(refId) {
         return this.seqIdToOriginalRefName[refId];
@@ -155,44 +155,37 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         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 { cram } = await this.setup(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));
+            if (refId === undefined) {
+                console.warn('Unknown refName', refName);
+                observer.complete();
+                return;
+            }
+            if (originalRefName) {
+                this.seqIdToOriginalRefName[refId] = originalRefName;
+            }
+            statusCallback('Downloading alignments');
+            const records = await cram.getRecordsForRange(refId, start, end);
+            checkAbortSignal(signal);
+            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+            let filtered = records.filter(record => {
+                const flags = record.flags;
+                return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
+            });
+            if (tagFilter) {
+                filtered = filtered.filter(record => {
+                    // @ts-ignore
+                    const val = record[tagFilter.tag];
+                    return val === '*' ? val !== undefined : val === tagFilter.value;
                 });
             }
-            else {
-                console.warn('Unknown refName', refName);
+            if (readName) {
+                filtered = filtered.filter(record => record.readName === readName);
             }
+            filtered.forEach(record => {
+                observer.next(this.cramRecordToFeature(record));
+            });
             statusCallback('');
             observer.complete();
         }, signal);
@@ -220,7 +213,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         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 chrId !== undefined
+                ? cram.index.getEntriesForRange(chrId, start, end)
+                : [{ sliceBytes: 0 }];
         }));
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }

package/esm/CramAdapter/CramAdapter.js.map

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

@@ -1,4 +1,5 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
 export interface Mismatch {
     qual?: number;
@@ -13,28 +14,28 @@ export interface Mismatch {
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
-    constructor(record: any, _store: CramAdapter);
-    _get_name(): any;
+    constructor(record: CramRecord, _store: CramAdapter);
+    _get_name(): string | undefined;
     _get_start(): number;
     _get_end(): number;
-    _get_cram_read_features(): any;
+    _get_cram_read_features(): import("@gmod/cram/dist/cramFile/record").ReadFeature[] | undefined;
     _get_type(): string;
-    _get_score(): any;
-    _get_flags(): any;
+    _get_score(): number | undefined;
+    _get_flags(): number;
     _get_strand(): 1 | -1;
-    _read_group_id(): number | undefined;
-    _get_qual(): any;
-    qualRaw(): any;
+    _read_group_id(): string | undefined;
+    _get_qual(): string;
+    qualRaw(): number[] | null | undefined;
     _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
-    _get_pair_orientation(): any;
-    _get_template_length(): any;
+    _get_pair_orientation(): string | null | undefined;
+    _get_template_length(): number | undefined;
     _get_next_seq_id(): string | undefined;
-    _get_next_pos(): any;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
-    _get_tags(): any;
-    _get_seq(): any;
+    _get_tags(): Record<string, string>;
+    _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,7 +1,6 @@
 export default class CramSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(record, _store) {
         this.record = record;
         this._store = _store;
@@ -13,7 +12,8 @@ export default class CramSlightlyLazyFeature {
         return this.record.alignmentStart - 1;
     }
     _get_end() {
-        return this.record.alignmentStart + this.record.lengthOnRef - 1;
+        var _a;
+        return this.record.alignmentStart + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1) - 1;
     }
     _get_cram_read_features() {
         return this.record.readFeatures;
@@ -83,12 +83,16 @@ export default class CramSlightlyLazyFeature {
         let cigar = '';
         let op = 'M';
         let oplen = 0;
+        if (!this.record._refRegion) {
+            return '';
+        }
         // not sure I should access these, but...
         const ref = this.record._refRegion.seq;
         const refStart = this.record._refRegion.start;
         let last_pos = this.record.alignmentStart;
         let sublen = 0;
         if (typeof this.record.readFeatures !== 'undefined') {
+            let insLen = 0;
             // @ts-ignore
             for (let i = 0; i < this.record.readFeatures.length; i++) {
                 const { code, refPos, sub, data } = this.record.readFeatures[i];
@@ -103,6 +107,10 @@ export default class CramSlightlyLazyFeature {
                     op = 'M';
                     oplen += sublen;
                 }
+                if (insLen > 0 && code !== 'i') {
+                    cigar += `${insLen}I`;
+                    insLen = 0;
+                }
                 if (code === 'b') {
                     // An array of bases stored verbatim
                     const ret = data.split(',');
@@ -143,11 +151,11 @@ export default class CramSlightlyLazyFeature {
                 }
                 else if (code === 'i') {
                     // Single base insertion
-                    seq += data;
+                    // seq += data
                     if (oplen) {
                         cigar += oplen + op;
                     }
-                    cigar += `${1}I`;
+                    insLen++;
                     oplen = 0;
                 }
                 else if (code === 'P') {
@@ -229,18 +237,10 @@ export default class CramSlightlyLazyFeature {
         return 0;
     }
     toJSON() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const tags = {};
-        this.tags().forEach((t) => {
-            const val = this.get(t);
-            if (val !== undefined) {
-                tags[t] = val;
-            }
-        });
         return {
-            ...tags,
-            name: this.get('name'),
-            type: this.get('type'),
+            ...Object.fromEntries(this.tags()
+                .map(t => [t, this.get(t)])
+                .filter(elt => elt[1] !== undefined)),
             uniqueId: this.id(),
         };
     }
@@ -253,10 +253,21 @@ export default class CramSlightlyLazyFeature {
         const start = this.get('start');
         const mismatches = new Array(readFeatures.length);
         let j = 0;
+        let insLen = 0;
+        let refPos = 0;
         for (let i = 0; i < readFeatures.length; i++) {
             const f = readFeatures[i];
             const { code, pos, data, sub, ref } = f;
-            const refPos = f.refPos - 1 - start;
+            if (insLen > 0 && code !== 'i') {
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: `${insLen}`,
+                    length: 0,
+                };
+                insLen = 0;
+            }
+            refPos = f.refPos - 1 - start;
             if (code === 'X') {
                 // substitution
                 mismatches[j++] = {
@@ -332,12 +343,7 @@ export default class CramSlightlyLazyFeature {
             else if (code === 'i') {
                 // single-base insertion
                 // insertion
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: data,
-                    length: 1,
-                };
+                insLen++;
             }
             else if (code === 'Q') {
                 // single quality value

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
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package/esm/CramAdapter/configSchema.d.ts

@@ -1,3 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/CramAdapter/configSchema.js

@@ -1,26 +1,48 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-export default (pluginManager) => {
-    return types.late(() => ConfigurationSchema('CramAdapter', {
-        fetchSizeLimit: {
-            type: 'number',
-            defaultValue: 3000000,
+/**
+ * #config CramAdapter
+ * used to configure CRAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('CramAdapter', {
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: 'number',
+        description: 'used to determine when to display a warning to the user that too much data will be fetched',
+        defaultValue: 3000000,
+    },
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram',
+            locationType: 'UriLocation',
         },
-        cramLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram',
-                locationType: 'UriLocation',
-            },
+    },
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram.crai',
+            locationType: 'UriLocation',
         },
-        craiLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram.crai',
-                locationType: 'UriLocation',
-            },
-        },
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true }));
-};
+    },
+    /**
+     * #slot sequenceAdapter
+     * 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',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true });
+export default configSchema;
 //# sourceMappingURL=configSchema.js.map