@jbrowse/plugin-bed 2.2.0 → 2.2.2

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -0,0 +1,25 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature, SimpleFeature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
+export default class BedpeAdapter extends BaseFeatureDataAdapter {
+    protected bedpeFeatures?: Promise<{
+        header: string;
+        feats1: Record<string, string[]>;
+        feats2: Record<string, string[]>;
+        columnNames: string[];
+    }>;
+    protected intervalTrees: {
+        [key: string]: Promise<IntervalTree | undefined> | undefined;
+    };
+    static capabilities: string[];
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureTreeP;
+    private loadFeatureTree;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -0,0 +1,173 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { SimpleFeature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+import { unzip } from '@gmod/bgzf-filehandle';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export function featureData(line, uniqueId, flip, names) {
+    const l = line.split('\t');
+    const ref1 = l[flip ? 3 : 0];
+    const start1 = +l[flip ? 4 : 1];
+    const end1 = +l[flip ? 5 : 2];
+    const ref2 = +l[!flip ? 3 : 0];
+    const start2 = +l[!flip ? 4 : 1];
+    const end2 = +l[!flip ? 5 : 2];
+    const name = l[6];
+    const score = +l[7];
+    const strand1 = parseStrand(l[8]);
+    const strand2 = parseStrand(l[9]);
+    const extra = l.slice(9);
+    const rest = names
+        ? Object.fromEntries(names.slice(9).map((n, idx) => [n, extra[idx]]))
+        : extra;
+    return new SimpleFeature({
+        start: start1,
+        end: end1,
+        refName: ref1,
+        strand: strand1,
+        name,
+        ...rest,
+        score,
+        uniqueId,
+        mate: { refName: ref2, start: start2, end: end2, strand: strand2 },
+    });
+}
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else if (strand === '.') {
+        return 0;
+    }
+    else {
+        return undefined;
+    }
+}
+export default class BedpeAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedpeLocation');
+        const buf = await openLocation(bedLoc, pm).readFile(opts);
+        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        // 512MB  max chrome string length is 512MB
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const headerLines = [];
+        let i = 0;
+        for (; i < lines.length && lines[i].startsWith('#'); i++) {
+            headerLines.push(lines[i]);
+        }
+        const header = headerLines.join('\n');
+        const feats1 = {};
+        const feats2 = {};
+        for (; i < lines.length; i++) {
+            const line = lines[i];
+            const cols = line.split('\t');
+            const r1 = cols[0];
+            const r2 = cols[3];
+            if (!feats1[r1]) {
+                feats1[r1] = [];
+            }
+            if (!feats2[r2]) {
+                feats2[r2] = [];
+            }
+            feats1[r1].push(line);
+            feats2[r2].push(line);
+        }
+        const columnNames = this.getConf('columnNames');
+        return {
+            header,
+            feats1,
+            feats2,
+            columnNames,
+        };
+    }
+    async loadData(opts = {}) {
+        if (!this.bedpeFeatures) {
+            this.bedpeFeatures = this.loadDataP(opts).catch(e => {
+                this.bedpeFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.bedpeFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { feats1, feats2 } = await this.loadData(opts);
+        return [...new Set([...Object.keys(feats1), ...Object.keys(feats2)])];
+    }
+    async getHeader(opts = {}) {
+        const { header } = await this.loadData(opts);
+        return header;
+    }
+    async getNames() {
+        const { header, columnNames } = await this.loadData();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
+        const defline = defs[defs.length - 1];
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(field => field.trim())
+            : undefined;
+    }
+    async loadFeatureTreeP(refName) {
+        const { feats1, feats2 } = await this.loadData();
+        const lines1 = feats1[refName];
+        const lines2 = feats2[refName];
+        const names = await this.getNames();
+        const intervalTree = new IntervalTree();
+        const ret1 = lines1 === null || lines1 === void 0 ? void 0 : lines1.map((f, i) => {
+            const uniqueId = `${this.id}-${refName}-${i}`;
+            return featureData(f, uniqueId, false, names);
+        });
+        const ret2 = lines2 === null || lines2 === void 0 ? void 0 : lines2.map((f, i) => {
+            const uniqueId = `${this.id}-${refName}-${i}`;
+            return featureData(f, uniqueId, true, names);
+        });
+        for (let i = 0; i < ret1.length; i++) {
+            const obj = ret1[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        for (let i = 0; i < ret2.length; i++) {
+            const obj = ret2[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        return intervalTree;
+    }
+    async loadFeatureTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(e => {
+                this.intervalTrees[refName] = undefined;
+                throw e;
+            });
+        }
+        return this.intervalTrees[refName];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            const intervalTree = await this.loadFeatureTree(refName);
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => observer.next(f));
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
+//# sourceMappingURL=BedpeAdapter.js.map

package/esm/BedpeAdapter/BedpeAdapter.js.map

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

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

package/esm/BedpeAdapter/configSchema.js

@@ -0,0 +1,29 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config BedpeAdapter
+ * intended for SVs in a single assembly
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
+    /**
+     * #slot
+     * can be plaintext or gzipped, not indexed so loaded into memory on startup
+     */
+    bedpeLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedpe.gz',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+export default BedpeAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/BedpeAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedpeAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,cAAc,EACd;IACE;;;OAGG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,sBAAsB;YAC3B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,YAAY,CAAA"}

package/esm/BedpeAdapter/index.d.ts

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

package/esm/BedpeAdapter/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: 'BedpeAdapter',
+        configSchema,
+        getAdapterClass: () => import('./BedpeAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/BedpeAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedpeAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,cAAc;QACpB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,gBAAgB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/BigBedAdapter/index.d.ts

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

package/esm/BigBedAdapter/index.js

@@ -1,2 +1,10 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BigBedAdapter',
+        configSchema,
+        getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/BigBedAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigBedAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigBedAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/index.js

@@ -1,8 +1,8 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import Plugin from '@jbrowse/core/Plugin';
-import { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter';
-import { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter';
-import { configSchema as bedAdapterConfigSchema } from './BedAdapter';
+import BigBedAdapterF from './BigBedAdapter';
+import BedpeAdapterF from './BedpeAdapter';
+import BedTabixAdapterF from './BedTabixAdapter';
+import BedAdapterF from './BedAdapter';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default class BedPlugin extends Plugin {
     constructor() {
@@ -10,11 +10,10 @@ export default class BedPlugin extends Plugin {
         this.name = 'BedPlugin';
     }
     install(pluginManager) {
-        pluginManager.addAdapterType(() => new AdapterType({
-            name: 'BigBedAdapter',
-            configSchema: bigBedAdapterConfigSchema,
-            getAdapterClass: () => import('./BigBedAdapter/BigBedAdapter').then(r => r.default),
-        }));
+        BigBedAdapterF(pluginManager);
+        BedAdapterF(pluginManager);
+        BedpeAdapterF(pluginManager);
+        BedTabixAdapterF(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.(bb|bigbed)$/i;
@@ -33,16 +32,20 @@ export default class BedPlugin extends Plugin {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
-        pluginManager.addAdapterType(() => new AdapterType({
-            name: 'BedTabixAdapter',
-            configSchema: bedTabixAdapterConfigSchema,
-            getAdapterClass: () => import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),
-        }));
-        pluginManager.addAdapterType(() => new AdapterType({
-            name: 'BedAdapter',
-            configSchema: bedAdapterConfigSchema,
-            getAdapterClass: () => import('./BedAdapter/BedAdapter').then(r => r.default),
-        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.bedpe\.gz$/i;
+                const adapterName = 'BedpeAdapter';
+                const fileName = getFileName(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedpeLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.bed\.b?gz$/i;

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,GAEd,MAAM,2BAA2B,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,MAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IAwGpB,CAAC;IAtGC,OAAO,CAAC,aAA4B;QAClC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,WAAW,CAAC,aAAa,CAAC,CAAA;QAC1B,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,cAAc,CAAA;gBAClC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;qBACpB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,eAAe,CAAA;gBAClC,MAAM,WAAW,GAAG,iBAAiB,CAAA;gBACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;gBAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,aAAa,EAAE,IAAI;wBACnB,KAAK,EAAE;4BACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;yBAClD;qBACF,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,SAAS,CAAA;gBAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,WAAW,EAAE,IAAI;qBAClB,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.2.0",
+  "version": "2.2.2",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/bed",
     "prepublishOnly": "yarn test",
-    "prepack": "yarn build; yarn useDist",
+    "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
 }