@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -0,0 +1,349 @@
+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;
+    }
+    _get_name() {
+        return this.record.readName;
+    }
+    _get_start() {
+        return this.record.alignmentStart - 1;
+    }
+    _get_end() {
+        return this.record.alignmentStart + this.record.lengthOnRef - 1;
+    }
+    _get_cram_read_features() {
+        return this.record.readFeatures;
+    }
+    _get_type() {
+        return 'match';
+    }
+    _get_score() {
+        return this.record.mappingQuality;
+    }
+    _get_flags() {
+        return this.record.flags;
+    }
+    _get_strand() {
+        return this.record.isReverseComplemented() ? -1 : 1;
+    }
+    _read_group_id() {
+        const rg = this._store.samHeader.readGroups;
+        return rg ? rg[this.record.readGroupId] : undefined;
+    }
+    _get_qual() {
+        return (this.record.qualityScores || []).join(' ');
+    }
+    qualRaw() {
+        return this.record.qualityScores;
+    }
+    _get_seq_id() {
+        return this._store.refIdToName(this.record.sequenceId);
+    }
+    _get_refName() {
+        return this._get_seq_id();
+    }
+    _get_is_paired() {
+        return !!this.record.mate;
+    }
+    _get_pair_orientation() {
+        return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
+    }
+    _get_template_length() {
+        return this.record.templateLength || this.record.templateSize;
+    }
+    _get_next_seq_id() {
+        return this.record.mate
+            ? this._store.refIdToName(this.record.mate.sequenceId)
+            : undefined;
+    }
+    _get_next_pos() {
+        return this.record.mate ? this.record.mate.alignmentStart : undefined;
+    }
+    _get_next_segment_position() {
+        return this.record.mate
+            ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
+            : undefined;
+    }
+    _get_tags() {
+        const RG = this._read_group_id();
+        const { tags } = this.record;
+        // avoids a tag copy if no RG, but just copy if there is one
+        return RG !== undefined ? { ...tags, RG } : tags;
+    }
+    _get_seq() {
+        return this.record.getReadBases();
+    }
+    // generate a CIGAR, based on code from jkbonfield
+    _get_CIGAR() {
+        let seq = '';
+        let cigar = '';
+        let op = 'M';
+        let oplen = 0;
+        // 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') {
+            // @ts-ignore
+            for (let i = 0; i < this.record.readFeatures.length; i++) {
+                const { code, refPos, sub, data } = this.record.readFeatures[i];
+                sublen = refPos - last_pos;
+                seq += ref.substring(last_pos - refStart, refPos - refStart);
+                last_pos = refPos;
+                if (oplen && op !== 'M') {
+                    cigar += oplen + op;
+                    oplen = 0;
+                }
+                if (sublen) {
+                    op = 'M';
+                    oplen += sublen;
+                }
+                if (code === 'b') {
+                    // An array of bases stored verbatim
+                    const ret = data.split(',');
+                    const added = String.fromCharCode(...ret);
+                    seq += added;
+                    last_pos += added.length;
+                    oplen += added.length;
+                }
+                else if (code === 'B') {
+                    // Single base (+ qual score)
+                    seq += sub;
+                    last_pos++;
+                    oplen++;
+                }
+                else if (code === 'X') {
+                    // Substitution
+                    seq += sub;
+                    last_pos++;
+                    oplen++;
+                }
+                else if (code === 'D' || code === 'N') {
+                    // Deletion or Ref Skip
+                    last_pos += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += data + code;
+                    oplen = 0;
+                }
+                else if (code === 'I' || code === 'S') {
+                    // Insertion or soft-clip
+                    seq += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += data.length + code;
+                    oplen = 0;
+                }
+                else if (code === 'i') {
+                    // Single base insertion
+                    seq += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += `${1}I`;
+                    oplen = 0;
+                }
+                else if (code === 'P') {
+                    // Padding
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += `${data}P`;
+                }
+                else if (code === 'H') {
+                    // Hard clip
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += `${data}H`;
+                    oplen = 0;
+                } // else q or Q
+            }
+        }
+        else {
+            sublen = this.record.readLength - seq.length;
+        }
+        if (seq.length !== this.record.readLength) {
+            sublen = this.record.readLength - seq.length;
+            seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen);
+            if (oplen && op !== 'M') {
+                cigar += oplen + op;
+                oplen = 0;
+            }
+            op = 'M';
+            oplen += sublen;
+        }
+        if (oplen) {
+            cigar += oplen + op;
+        }
+        return cigar;
+    }
+    tags() {
+        const properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
+        return properties
+            .filter(prop => prop.startsWith('_get_') &&
+            prop !== '_get_mismatches' &&
+            prop !== '_get_cram_read_features')
+            .map(methodName => methodName.replace('_get_', ''));
+    }
+    id() {
+        return `${this._store.id}-${this.record.uniqueId}`;
+    }
+    get(field) {
+        const methodName = `_get_${field}`;
+        // @ts-ignore
+        if (this[methodName]) {
+            // @ts-ignore
+            return this[methodName]();
+        }
+        return undefined;
+    }
+    parent() {
+        return undefined;
+    }
+    children() {
+        return undefined;
+    }
+    set() { }
+    pairedFeature() {
+        return false;
+    }
+    _get_clipPos() {
+        const mismatches = this.get('mismatches');
+        if (mismatches.length) {
+            const record = this.get('strand') === -1
+                ? mismatches[mismatches.length - 1]
+                : mismatches[0];
+            const { type, cliplen } = record;
+            if (type === 'softclip' || type === 'hardclip') {
+                return cliplen;
+            }
+        }
+        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'),
+            uniqueId: this.id(),
+        };
+    }
+    _get_mismatches() {
+        const readFeatures = this.get('cram_read_features');
+        const qual = this.qualRaw();
+        if (!readFeatures) {
+            return [];
+        }
+        const start = this.get('start');
+        const mismatches = new Array(readFeatures.length);
+        let j = 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 (code === 'X') {
+                // substitution
+                mismatches[j++] = {
+                    start: refPos,
+                    length: 1,
+                    base: sub,
+                    qual: qual === null || qual === void 0 ? void 0 : qual[pos],
+                    altbase: ref,
+                    type: 'mismatch',
+                };
+            }
+            else if (code === 'I') {
+                // insertion
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: `${data.length}`,
+                    length: 0,
+                };
+            }
+            else if (code === 'N') {
+                // reference skip
+                mismatches[j++] = {
+                    type: 'skip',
+                    length: data,
+                    start: refPos,
+                    base: 'N',
+                };
+            }
+            else if (code === 'S') {
+                // soft clip
+                const len = data.length;
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'softclip',
+                    base: `S${len}`,
+                    cliplen: len,
+                    length: 1,
+                };
+            }
+            else if (code === 'P') {
+                // padding
+            }
+            else if (code === 'H') {
+                // hard clip
+                const len = data;
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'hardclip',
+                    base: `H${len}`,
+                    cliplen: len,
+                    length: 1,
+                };
+            }
+            else if (code === 'D') {
+                // deletion
+                mismatches[j++] = {
+                    type: 'deletion',
+                    length: data,
+                    start: refPos,
+                    base: '*',
+                };
+            }
+            else if (code === 'b') {
+                // stretch of bases
+            }
+            else if (code === 'q') {
+                // stretch of qual scores
+            }
+            else if (code === 'B') {
+                // a pair of [base, qual]
+            }
+            else if (code === 'i') {
+                // single-base insertion
+                // insertion
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: data,
+                    length: 1,
+                };
+            }
+            else if (code === 'Q') {
+                // single quality value
+            }
+        }
+        return mismatches.slice(0, j);
+    }
+}
+//# sourceMappingURL=CramSlightlyLazyFeature.js.map

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

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

@@ -0,0 +1,29 @@
+import { GenericFilehandle } from 'generic-filehandle';
+import { Observable } from 'rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare function parseSmallFasta(text: string): {
+    id: string;
+    description: string;
+    sequence: string;
+}[];
+declare type FileHandle = GenericFilehandle;
+export declare class FetchableSmallFasta {
+    data: Promise<ReturnType<typeof parseSmallFasta>>;
+    constructor(filehandle: FileHandle);
+    fetch(id: number, start: number, end: number): Promise<string>;
+    getSequenceList(): Promise<string[]>;
+}
+export declare class SequenceAdapter extends BaseFeatureDataAdapter {
+    fasta: FetchableSmallFasta;
+    refNames: string[];
+    constructor(filehandle: FileHandle);
+    getRefNames(): Promise<string[]>;
+    getFeatures({ refName, start, end, }: {
+        refName: string;
+        start: number;
+        end: number;
+    }): Observable<SimpleFeature>;
+    freeResources(): void;
+}
+export {};

package/esm/CramAdapter/CramTestAdapters.js

@@ -0,0 +1,70 @@
+import { Observable } from 'rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ConfigurationSchema } from '@jbrowse/core/configuration/configurationSchema';
+// setup for Cram Adapter Testing
+export function parseSmallFasta(text) {
+    return text
+        .split('>')
+        .filter(t => /\S/.test(t))
+        .map(entryText => {
+        const [defLine, ...seqLines] = entryText.split('\n');
+        const [id, ...descriptionLines] = defLine.split(' ');
+        const description = descriptionLines.join(' ');
+        const sequence = seqLines.join('').replace(/\s/g, '');
+        return { id, description, sequence };
+    });
+}
+export class FetchableSmallFasta {
+    constructor(filehandle) {
+        this.data = filehandle.readFile().then(buffer => {
+            const text = buffer.toString('utf8');
+            return parseSmallFasta(text);
+        });
+    }
+    async fetch(id, start, end) {
+        const data = await this.data;
+        const entry = data[id];
+        const length = end - start + 1;
+        if (!entry) {
+            throw new Error(`no sequence with id ${id} exists`);
+        }
+        return entry.sequence.substr(start - 1, length);
+    }
+    async getSequenceList() {
+        const data = await this.data;
+        return data.map(entry => entry.id);
+    }
+}
+export class SequenceAdapter extends BaseFeatureDataAdapter {
+    constructor(filehandle) {
+        super(ConfigurationSchema('empty', {}).create());
+        this.refNames = [];
+        this.fasta = new FetchableSmallFasta(filehandle);
+    }
+    async getRefNames() {
+        return this.refNames;
+    }
+    getFeatures({ refName, start, end, }) {
+        return new Observable(observer => {
+            this.fasta
+                .getSequenceList()
+                .then(refNames => {
+                this.refNames = refNames;
+            })
+                .then(() => this.fasta.fetch(this.refNames.indexOf(refName), start, end))
+                .then(ret => {
+                observer.next(new SimpleFeature({
+                    uniqueId: `${refName}-${start}-${end}`,
+                    seq: ret,
+                    start,
+                    end,
+                }));
+                observer.complete();
+            });
+            return { unsubscribe: () => { } };
+        });
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=CramTestAdapters.js.map

package/esm/CramAdapter/CramTestAdapters.js.map

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

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

package/esm/CramAdapter/configSchema.js

@@ -0,0 +1,26 @@
+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,
+        },
+        cramLocation: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.cram',
+                locationType: 'UriLocation',
+            },
+        },
+        craiLocation: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.cram.crai',
+                locationType: 'UriLocation',
+            },
+        },
+        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    }, { explicitlyTyped: true }));
+};
+//# sourceMappingURL=configSchema.js.map

package/esm/CramAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,OAAO,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACrB,mBAAmB,CACjB,aAAa,EACb;QACE,cAAc,EAAE;YACd,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,OAAS;SACxB;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,kBAAkB;gBACvB,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,uBAAuB;gBAC5B,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA;AACH,CAAC,CAAA"}

package/esm/CramAdapter/index.d.ts

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

package/esm/CramAdapter/index.js

@@ -0,0 +1,11 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+// locals
+import configSchemaF from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'CramAdapter',
+        configSchema: pluginManager.load(configSchemaF),
+        getAdapterClass: () => import('./CramAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/CramAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,aAAa,CAAC;QAC/C,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -0,0 +1,9 @@
+import { BamFile } from '@gmod/bam';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BamAdapter from '../BamAdapter/BamAdapter';
+export default class HtsgetBamAdapter extends BamAdapter {
+    protected configure(): Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+    }>;
+}

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -0,0 +1,27 @@
+import { HtsgetFile } from '@gmod/bam';
+import { readConfObject } from '@jbrowse/core/configuration';
+import BamAdapter from '../BamAdapter/BamAdapter';
+export default class HtsgetBamAdapter extends BamAdapter {
+    async configure() {
+        if (!this.configured) {
+            const htsgetBase = readConfObject(this.config, 'htsgetBase');
+            const htsgetTrackId = readConfObject(this.config, 'htsgetTrackId');
+            const bam = new HtsgetFile({
+                baseUrl: htsgetBase,
+                trackId: htsgetTrackId,
+            });
+            const adapterConfig = readConfObject(this.config, 'sequenceAdapter');
+            if (adapterConfig && this.getSubAdapter) {
+                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => {
+                    return {
+                        bam,
+                        sequenceAdapter: dataAdapter,
+                    };
+                });
+            }
+            this.configured = Promise.resolve({ bam });
+        }
+        return this.configured;
+    }
+}
+//# sourceMappingURL=HtsgetBamAdapter.js.map

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,WAAW,CAAA;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAE5D,OAAO,UAAU,MAAM,0BAA0B,CAAA;AAEjD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,UAAU;IAC5C,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,MAAM,UAAU,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;YAC5D,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;YAClE,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC;gBACzB,OAAO,EAAE,UAAU;gBACnB,OAAO,EAAE,aAAa;aACvB,CAAuB,CAAA;YAExB,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;YACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;gBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,CAAC,EAAE,WAAW,EAAE,EAAE,EAAE;oBAClB,OAAO;wBACL,GAAG;wBACH,eAAe,EAAE,WAAqC;qBACvD,CAAA;gBACH,CAAC,CACF,CAAA;aACF;YACD,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;SAC3C;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;CACF"}

package/esm/HtsgetBamAdapter/configSchema.d.ts

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

package/esm/HtsgetBamAdapter/configSchema.js

@@ -0,0 +1,17 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export default types.late(() => ConfigurationSchema('HtsgetBamAdapter', {
+    htsgetBase: {
+        type: 'string',
+        defaultValue: '',
+    },
+    htsgetTrackId: {
+        type: 'string',
+        defaultValue: '',
+    },
+    sequenceAdapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true }));
+//# sourceMappingURL=configSchema.js.map

package/esm/HtsgetBamAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/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,kBAAkB,EAClB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}

package/esm/HtsgetBamAdapter/index.d.ts

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

package/esm/HtsgetBamAdapter/index.js

@@ -0,0 +1,16 @@
+import configSchema from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'HtsgetBamAdapter',
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        configSchema,
+        getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/HtsgetBamAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AlignmentsDisplayModel } from '../models/model';
+declare function AlignmentsDisplay({ model }: {
+    model: AlignmentsDisplayModel;
+}): JSX.Element;
+declare const _default: typeof AlignmentsDisplay;
+export default _default;