@jbrowse/plugin-bed 1.7.11 → 2.1.0

package/dist/util.js

@@ -1,183 +1,164 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.featureData = featureData;
-exports.ucscProcessedTranscript = ucscProcessedTranscript;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _util = require("@jbrowse/core/util");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = exports.ucscProcessedTranscript = void 0;
+var util_1 = require("@jbrowse/core/util");
 function ucscProcessedTranscript(feature) {
-  var children = feature.children(); // split the blocks into UTR, CDS, and exons
-
-  var thickStart = feature.get('thickStart');
-  var thickEnd = feature.get('thickEnd');
-
-  if (!thickStart && !thickEnd) {
-    return feature;
-  }
-
-  var blocks = children ? children.filter(function (child) {
-    return child.get('type') === 'block';
-  }).sort(function (a, b) {
-    return a.get('start') - b.get('start');
-  }) : []; // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  var newChildren = [];
-  blocks.forEach(function (block) {
-    var start = block.get('start');
-    var end = block.get('end');
-
-    if (thickStart >= end) {
-      // left-side UTR
-      var prime = feature.get('strand') > 0 ? 'five' : 'three';
-      newChildren.push({
-        type: "".concat(prime, "_prime_UTR"),
-        start: start,
-        end: end
-      });
-    } else if (thickStart > start && thickStart < end && thickEnd >= end) {
-      // UTR | CDS
-      var _prime = feature.get('strand') > 0 ? 'five' : 'three';
-
-      newChildren.push({
-        type: "".concat(_prime, "_prime_UTR"),
-        start: start,
-        end: thickStart
-      }, {
-        type: 'CDS',
-        start: thickStart,
-        end: end
-      });
-    } else if (thickStart <= start && thickEnd >= end) {
-      // CDS
-      newChildren.push({
-        type: 'CDS',
-        start: start,
-        end: end
-      });
-    } else if (thickStart > start && thickStart < end && thickEnd < end) {
-      // UTR | CDS | UTR
-      var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
-      var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
-      newChildren.push({
-        type: "".concat(leftPrime, "_prime_UTR"),
-        start: start,
-        end: thickStart
-      }, {
-        type: "CDS",
-        start: thickStart,
-        end: thickEnd
-      }, {
-        type: "".concat(rightPrime, "_prime_UTR"),
-        start: thickEnd,
-        end: end
-      });
-    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-      // CDS | UTR
-      var _prime2 = feature.get('strand') > 0 ? 'three' : 'five';
-
-      newChildren.push({
-        type: "CDS",
-        start: start,
-        end: thickEnd
-      }, {
-        type: "".concat(_prime2, "_prime_UTR"),
-        start: thickEnd,
-        end: end
-      });
-    } else if (thickEnd <= start) {
-      // right-side UTR
-      var _prime3 = feature.get('strand') > 0 ? 'three' : 'five';
-
-      newChildren.push({
-        type: "".concat(_prime3, "_prime_UTR"),
-        start: start,
-        end: end
-      });
+    var children = feature.children();
+    // split the blocks into UTR, CDS, and exons
+    var thickStart = feature.get('thickStart');
+    var thickEnd = feature.get('thickEnd');
+    if (!thickStart && !thickEnd) {
+        return feature;
     }
-  });
-  var newData = Object.fromEntries(feature.tags().map(function (tag) {
-    return [tag, feature.get(tag)];
-  }));
-  newData.subfeatures = newChildren;
-  newData.type = 'mRNA';
-  newData.uniqueId = feature.id();
-  delete newData.chromStarts;
-  delete newData.chromStart;
-  delete newData.chromEnd;
-  delete newData.chrom;
-  delete newData.blockStarts;
-  delete newData.blockSizes;
-  delete newData.blockCount;
-  delete newData.thickStart;
-  delete newData.thickEnd;
-  var newFeature = new _util.SimpleFeature({
-    data: newData,
-    id: feature.id()
-  });
-  return newFeature;
+    var blocks = children
+        ? children
+            .filter(function (child) { return child.get('type') === 'block'; })
+            .sort(function (a, b) { return a.get('start') - b.get('start'); })
+        : [];
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    var newChildren = [];
+    blocks.forEach(function (block) {
+        var start = block.get('start');
+        var end = block.get('end');
+        if (thickStart >= end) {
+            // left-side UTR
+            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: end,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd >= end) {
+            // UTR | CDS
+            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: thickStart,
+            }, {
+                type: 'CDS',
+                start: thickStart,
+                end: end,
+            });
+        }
+        else if (thickStart <= start && thickEnd >= end) {
+            // CDS
+            newChildren.push({
+                type: 'CDS',
+                start: start,
+                end: end,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd < end) {
+            // UTR | CDS | UTR
+            var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
+            var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "".concat(leftPrime, "_prime_UTR"),
+                start: start,
+                end: thickStart,
+            }, {
+                type: "CDS",
+                start: thickStart,
+                end: thickEnd,
+            }, {
+                type: "".concat(rightPrime, "_prime_UTR"),
+                start: thickEnd,
+                end: end,
+            });
+        }
+        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+            // CDS | UTR
+            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "CDS",
+                start: start,
+                end: thickEnd,
+            }, {
+                type: "".concat(prime, "_prime_UTR"),
+                start: thickEnd,
+                end: end,
+            });
+        }
+        else if (thickEnd <= start) {
+            // right-side UTR
+            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: end,
+            });
+        }
+    });
+    var newData = Object.fromEntries(feature.tags().map(function (tag) { return [tag, feature.get(tag)]; }));
+    newData.subfeatures = newChildren;
+    newData.type = 'mRNA';
+    newData.uniqueId = feature.id();
+    delete newData.chromStarts;
+    delete newData.chromStart;
+    delete newData.chromEnd;
+    delete newData.chrom;
+    delete newData.blockStarts;
+    delete newData.blockSizes;
+    delete newData.blockCount;
+    delete newData.thickStart;
+    delete newData.thickEnd;
+    var newFeature = new util_1.SimpleFeature({
+        data: newData,
+        id: feature.id(),
+    });
+    return newFeature;
 }
-
+exports.ucscProcessedTranscript = ucscProcessedTranscript;
 function defaultParser(fields, line) {
-  return Object.fromEntries(line.split('\t').map(function (f, i) {
-    return [fields[i], f];
-  }));
+    return Object.fromEntries(line.split('\t').map(function (f, i) { return [fields[i], f]; }));
 }
-
 function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
-  var l = line.split('\t');
-  var refName = l[colRef];
-  var start = +l[colStart];
-  var colSame = colStart === colEnd ? 1 : 0;
-  var end = +l[colEnd] + colSame;
-  var data = names ? defaultParser(names, line) : parser.parseLine(line, {
-    uniqueId: uniqueId
-  });
-  var blockCount = data.blockCount,
-      blockSizes = data.blockSizes,
-      blockStarts = data.blockStarts,
-      chromStarts = data.chromStarts;
-
-  if (blockCount) {
-    var starts = chromStarts || blockStarts || [];
-    var sizes = blockSizes;
-    var blocksOffset = start;
-    data.subfeatures = [];
-
-    for (var b = 0; b < blockCount; b += 1) {
-      var bmin = (starts[b] || 0) + blocksOffset;
-      var bmax = bmin + (sizes[b] || 0);
-      data.subfeatures.push({
-        uniqueId: "".concat(uniqueId, "-").concat(b),
-        start: bmin,
-        end: bmax,
-        type: 'block'
-      });
+    var l = line.split('\t');
+    var refName = l[colRef];
+    var start = +l[colStart];
+    var colSame = colStart === colEnd ? 1 : 0;
+    var end = +l[colEnd] + colSame;
+    var data = names
+        ? defaultParser(names, line)
+        : parser.parseLine(line, { uniqueId: uniqueId });
+    var blockCount = data.blockCount, blockSizes = data.blockSizes, blockStarts = data.blockStarts, chromStarts = data.chromStarts;
+    if (blockCount) {
+        var starts = chromStarts || blockStarts || [];
+        var sizes = blockSizes;
+        var blocksOffset = start;
+        data.subfeatures = [];
+        for (var b = 0; b < blockCount; b += 1) {
+            var bmin = (starts[b] || 0) + blocksOffset;
+            var bmax = bmin + (sizes[b] || 0);
+            data.subfeatures.push({
+                uniqueId: "".concat(uniqueId, "-").concat(b),
+                start: bmin,
+                end: bmax,
+                type: 'block',
+            });
+        }
     }
-  }
-
-  if (scoreColumn) {
-    data.score = +data[scoreColumn];
-  }
-
-  delete data.chrom;
-  delete data.chromStart;
-  delete data.chromEnd;
-  var f = new _util.SimpleFeature(_objectSpread(_objectSpread({}, data), {}, {
-    start: start,
-    end: end,
-    refName: refName,
-    uniqueId: uniqueId
-  }));
-  return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
-}
+    if (scoreColumn) {
+        data.score = +data[scoreColumn];
+    }
+    delete data.chrom;
+    delete data.chromStart;
+    delete data.chromEnd;
+    var f = new util_1.SimpleFeature(__assign(__assign({}, data), { start: start, end: end, refName: refName, uniqueId: uniqueId }));
+    return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
+}
+exports.featureData = featureData;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

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package/esm/BedAdapter/BedAdapter.d.ts

@@ -0,0 +1,29 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
+    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 loadFeatureIntervalTreeHelper;
+    private loadFeatureIntervalTree;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/BedAdapter/BedAdapter.js

@@ -0,0 +1,130 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { featureData } from '../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 default class BedAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedLocation');
+        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').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 features = {};
+        for (; i < lines.length; i++) {
+            const line = lines[i];
+            const tab = line.indexOf('\t');
+            const refName = line.slice(0, tab);
+            if (!features[refName]) {
+                features[refName] = [];
+            }
+            features[refName].push(line);
+        }
+        const autoSql = this.getConf('autoSql');
+        const parser = new BED({ autoSql });
+        const columnNames = this.getConf('columnNames');
+        const scoreColumn = this.getConf('scoreColumn');
+        const colRef = this.getConf('colRef');
+        const colStart = this.getConf('colStart');
+        const colEnd = this.getConf('colEnd');
+        return {
+            header,
+            features,
+            parser,
+            columnNames,
+            scoreColumn,
+            colRef,
+            colStart,
+            colEnd,
+        };
+    }
+    async loadData(opts = {}) {
+        if (!this.bedFeatures) {
+            this.bedFeatures = this.loadDataP(opts).catch(e => {
+                this.bedFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.bedFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { features } = await this.loadData(opts);
+        return Object.keys(features);
+    }
+    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').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 loadFeatureIntervalTreeHelper(refName) {
+        const { colRef, colStart, colEnd, features, parser, scoreColumn } = await this.loadData();
+        const lines = features[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const names = await this.getNames();
+        const intervalTree = new IntervalTree();
+        const ret = lines.map((f, i) => {
+            const uniqueId = `${this.id}-${refName}-${i}`;
+            return featureData(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+        });
+        for (let i = 0; i < ret.length; i++) {
+            const obj = ret[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        return intervalTree;
+    }
+    async loadFeatureIntervalTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(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.loadFeatureIntervalTree(refName);
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => observer.next(f));
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
+//# sourceMappingURL=BedAdapter.js.map

package/esm/BedAdapter/BedAdapter.js.map

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package/esm/BedAdapter/configSchema.d.ts

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

package/esm/BedAdapter/configSchema.js

@@ -0,0 +1,38 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('BedAdapter', {
+    bedLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+    scoreColumn: {
+        type: 'string',
+        description: 'The column to use as a "score" attribute',
+        defaultValue: '',
+    },
+    autoSql: {
+        type: 'string',
+        description: 'The autoSql definition for the data fields in the file',
+        defaultValue: '',
+    },
+    colRef: {
+        type: 'number',
+        description: 'The column to use as a "refName" attribute',
+        defaultValue: 0,
+    },
+    colStart: {
+        type: 'number',
+        description: 'The column to use as a "start" attribute',
+        defaultValue: 1,
+    },
+    colEnd: {
+        type: 'number',
+        description: 'The column to use as a "end" attribute',
+        defaultValue: 2,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BedAdapter/configSchema.js.map

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

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/BedAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BedAdapter/index.js.map

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

@@ -0,0 +1,19 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import { TabixIndexedFile } from '@gmod/tabix';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class BedTabixAdapter extends BaseFeatureDataAdapter {
+    private parser;
+    protected bed: TabixIndexedFile;
+    protected columnNames: string[];
+    protected scoreColumn: string;
+    static capabilities: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}