@jbrowse/plugin-bed 2.18.0 → 3.0.0

package/dist/BedAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/BedGraphAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -77,6 +77,9 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     const start = +cols[colStart];
                     const end = +(same ? start + 1 : cols[colEnd]);
                     const rest = cols.slice(colEnd + 1);
+                    if (Number.isNaN(start) || Number.isNaN(end)) {
+                        throw new Error(`start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`);
+                    }
                     for (let j = 0; j < rest.length; j++) {
                         const uniqueId = `${this.id}-${fileOffset}-${j}`;
                         const score = Math.abs(+rest[j]);

package/dist/BedGraphTabixAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/BedTabixAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,9 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature } from '@jbrowse/core/util';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
-export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -3,75 +3,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = featureData;
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
-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(10);
-    const rest = names
-        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-        : extra;
-    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
-    return new util_1.SimpleFeature({
-        ...rest,
-        start: start1,
-        end: end1,
-        type: 'paired_feature',
-        refName: ref1,
-        strand: strand1,
-        name,
-        score,
-        uniqueId,
-        mate: {
-            refName: ref2,
-            start: start2,
-            end: end2,
-            strand: strand2,
-        },
-        ...(ALT ? { ALT: [ALT] } : {}),
-    });
-}
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    if (strand === '-') {
-        return -1;
-    }
-    if (strand === '.') {
-        return 0;
-    }
-    return undefined;
-}
+const util_2 = require("./util");
 class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.intervalTrees = {};
     }
     async loadDataP(opts) {
-        const pm = this.pluginManager;
-        const bedLoc = this.getConf('bedpeLocation');
-        const loc = (0, io_1.openLocation)(bedLoc, pm);
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const data = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(this.getConf('bedpeLocation'), this.pluginManager), opts);
         const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
         const headerLines = [];
         let i = 0;
@@ -139,8 +83,8 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { feats1, feats2 } = await this.loadData();
         const names = await this.getNames();
         const intervalTree = new interval_tree_1.default();
-        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
-        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
+        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
+        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
         for (const obj of [...ret1, ...ret2]) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);
         }

package/dist/BedpeAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/BedpeAdapter/util.d.ts

@@ -0,0 +1,2 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;

package/dist/BedpeAdapter/util.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = featureData;
+const util_1 = require("@jbrowse/core/util");
+const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
+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(10);
+    const rest = names
+        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
+        : {};
+    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
+    return new util_1.SimpleFeature({
+        ...rest,
+        start: start1,
+        end: end1,
+        type: 'paired_feature',
+        refName: ref1,
+        strand: strand1,
+        name,
+        score,
+        uniqueId,
+        mate: {
+            refName: ref2,
+            start: start2,
+            end: end2,
+            strand: strand2,
+        },
+        ...(ALT ? { ALT: [ALT] } : {}),
+    });
+}
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else if (strand === '.') {
+        return 0;
+    }
+    else {
+        return undefined;
+    }
+}

package/dist/BigBedAdapter/configSchema.js

@@ -15,7 +15,7 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
     aggregateField: {
         type: 'string',
         description: 'An attribute to aggregate features with',
-        defaultValue: 'geneName',
+        defaultValue: 'geneName2',
     },
 }, { explicitlyTyped: true });
 exports.default = BigBedAdapter;

package/dist/BigBedAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/dist/GuessAdapter/index.js

@@ -0,0 +1,68 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = GuessAdapterF;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = (0, tracks_1.getFileName)(file);
+            const indexName = index && (0, tracks_1.getFileName)(index);
+            if ((0, util_1.testAdapter)(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
+                return {
+                    type: 'BedpeAdapter',
+                    bedpeLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
+                (0, util_1.testAdapter)(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')) {
+                return {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
+                return {
+                    type: 'BedAdapter',
+                    bedLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
+                return {
+                    type: 'BedGraphAdapter',
+                    bedGraphLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
+                return {
+                    type: 'BedGraphTabixAdapter',
+                    bedGraphGzLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
+                return {
+                    type: 'BedTabixAdapter',
+                    bedGzLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => {
+        return ({
+            BedpeAdapter: 'VariantTrack',
+            BedGraphAdapter: 'QuantitativeTrack',
+            BedGraphTabixAdapter: 'QuantitativeTrack',
+        }[adapterName] || trackTypeGuesser(adapterName));
+    });
+}

package/dist/generateBedMethylFeature.js

@@ -3,7 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.isBedMethylFeature = isBedMethylFeature;
 exports.generateBedMethylFeature = generateBedMethylFeature;
 function isBedMethylFeature({ splitLine, start, end, }) {
-    return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
+    return (+(splitLine[6] || 0) === start &&
+        +(splitLine[7] || 0) === end &&
+        [9, 10, 11, 12, 13, 14, 15, 16, 17].every(r => splitLine[r] && !Number.isNaN(+splitLine[r])));
 }
 function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }) {
     const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = splitLine;

package/dist/generateRepeatMaskerFeature.js

@@ -30,8 +30,9 @@ function makeRepeatTrackDescription(description) {
     return { description };
 }
 function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
+    const { subfeatures, ...rest2 } = rest;
     return {
-        ...rest,
+        ...rest2,
         ...makeRepeatTrackDescription(description),
         uniqueId,
         refName,

package/dist/generateUcscTranscript.js

@@ -31,6 +31,7 @@ function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end,
                 refName,
@@ -39,6 +40,7 @@ function generateUcscTranscript(data) {
         else if (thickStart <= start && thickEnd >= end) {
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end,
                 refName,
@@ -52,6 +54,7 @@ function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end: thickEnd,
                 refName,
@@ -65,6 +68,7 @@ function generateUcscTranscript(data) {
         else if (thickStart <= start && thickEnd > start && thickEnd < end) {
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end: thickEnd,
                 refName,

package/dist/index.js

@@ -4,13 +4,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const BedAdapter_1 = __importDefault(require("./BedAdapter"));
 const BedGraphAdapter_1 = __importDefault(require("./BedGraphAdapter"));
 const BedGraphTabixAdapter_1 = __importDefault(require("./BedGraphTabixAdapter"));
 const BedTabixAdapter_1 = __importDefault(require("./BedTabixAdapter"));
 const BedpeAdapter_1 = __importDefault(require("./BedpeAdapter"));
 const BigBedAdapter_1 = __importDefault(require("./BigBedAdapter"));
+const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
 class BedPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -23,74 +23,7 @@ class BedPlugin extends Plugin_1.default {
         (0, BedTabixAdapter_1.default)(pluginManager);
         (0, BedGraphAdapter_1.default)(pluginManager);
         (0, BedGraphTabixAdapter_1.default)(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.(bb|bigbed)$/i;
-                const adapterName = 'BigBedAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const obj = {
-                    type: adapterName,
-                    bigBedLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bedpe(\.gz)?$/i;
-                const adapterName = 'BedpeAdapter';
-                const fileName = (0, tracks_1.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$/i;
-                const adapterName = 'BedTabixAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const indexName = index && (0, tracks_1.getFileName)(index);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedGzLocation: file,
-                        index: {
-                            location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                            indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                        },
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bed$/i;
-                const adapterName = 'BedAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => adapterName === 'BedpeAdapter'
-            ? 'VariantTrack'
-            : trackTypeGuesser(adapterName));
+        (0, GuessAdapter_1.default)(pluginManager);
     }
 }
 exports.default = BedPlugin;

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -75,6 +75,9 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
                     const start = +cols[colStart];
                     const end = +(same ? start + 1 : cols[colEnd]);
                     const rest = cols.slice(colEnd + 1);
+                    if (Number.isNaN(start) || Number.isNaN(end)) {
+                        throw new Error(`start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`);
+                    }
                     for (let j = 0; j < rest.length; j++) {
                         const uniqueId = `${this.id}-${fileOffset}-${j}`;
                         const score = Math.abs(+rest[j]);

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,9 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature } from '@jbrowse/core/util';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
-export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,71 +1,16 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
-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(10);
-    const rest = names
-        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-        : extra;
-    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
-    return new SimpleFeature({
-        ...rest,
-        start: start1,
-        end: end1,
-        type: 'paired_feature',
-        refName: ref1,
-        strand: strand1,
-        name,
-        score,
-        uniqueId,
-        mate: {
-            refName: ref2,
-            start: start2,
-            end: end2,
-            strand: strand2,
-        },
-        ...(ALT ? { ALT: [ALT] } : {}),
-    });
-}
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    if (strand === '-') {
-        return -1;
-    }
-    if (strand === '.') {
-        return 0;
-    }
-    return undefined;
-}
+import { featureData } from './util';
 class BedpeAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.intervalTrees = {};
     }
     async loadDataP(opts) {
-        const pm = this.pluginManager;
-        const bedLoc = this.getConf('bedpeLocation');
-        const loc = openLocation(bedLoc, pm);
-        const buffer = await fetchAndMaybeUnzip(loc, opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const data = await fetchAndMaybeUnzipText(openLocation(this.getConf('bedpeLocation'), this.pluginManager), opts);
         const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
         const headerLines = [];
         let i = 0;

package/esm/BedpeAdapter/util.d.ts

@@ -0,0 +1,2 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;

package/esm/BedpeAdapter/util.js

@@ -0,0 +1,52 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
+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(10);
+    const rest = names
+        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
+        : {};
+    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
+    return new SimpleFeature({
+        ...rest,
+        start: start1,
+        end: end1,
+        type: 'paired_feature',
+        refName: ref1,
+        strand: strand1,
+        name,
+        score,
+        uniqueId,
+        mate: {
+            refName: ref2,
+            start: start2,
+            end: end2,
+            strand: strand2,
+        },
+        ...(ALT ? { ALT: [ALT] } : {}),
+    });
+}
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else if (strand === '.') {
+        return 0;
+    }
+    else {
+        return undefined;
+    }
+}

package/esm/BigBedAdapter/configSchema.js

@@ -13,7 +13,7 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
     aggregateField: {
         type: 'string',
         description: 'An attribute to aggregate features with',
-        defaultValue: 'geneName',
+        defaultValue: 'geneName2',
     },
 }, { explicitlyTyped: true });
 export default BigBedAdapter;

package/esm/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/esm/GuessAdapter/index.js

@@ -0,0 +1,65 @@
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            if (testAdapter(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
+                return {
+                    type: 'BedpeAdapter',
+                    bedpeLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
+                testAdapter(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')) {
+                return {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
+                return {
+                    type: 'BedAdapter',
+                    bedLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
+                return {
+                    type: 'BedGraphAdapter',
+                    bedGraphLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
+                return {
+                    type: 'BedGraphTabixAdapter',
+                    bedGraphGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if (testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
+                return {
+                    type: 'BedTabixAdapter',
+                    bedGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => {
+        return ({
+            BedpeAdapter: 'VariantTrack',
+            BedGraphAdapter: 'QuantitativeTrack',
+            BedGraphTabixAdapter: 'QuantitativeTrack',
+        }[adapterName] || trackTypeGuesser(adapterName));
+    });
+}

package/esm/generateBedMethylFeature.js

@@ -1,5 +1,7 @@
 export function isBedMethylFeature({ splitLine, start, end, }) {
-    return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
+    return (+(splitLine[6] || 0) === start &&
+        +(splitLine[7] || 0) === end &&
+        [9, 10, 11, 12, 13, 14, 15, 16, 17].every(r => splitLine[r] && !Number.isNaN(+splitLine[r])));
 }
 export function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }) {
     const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = splitLine;

package/esm/generateRepeatMaskerFeature.js

@@ -26,8 +26,9 @@ function makeRepeatTrackDescription(description) {
     return { description };
 }
 export function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
+    const { subfeatures, ...rest2 } = rest;
     return {
-        ...rest,
+        ...rest2,
         ...makeRepeatTrackDescription(description),
         uniqueId,
         refName,

package/esm/generateUcscTranscript.js

@@ -27,6 +27,7 @@ export function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end,
                 refName,
@@ -35,6 +36,7 @@ export function generateUcscTranscript(data) {
         else if (thickStart <= start && thickEnd >= end) {
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end,
                 refName,
@@ -48,6 +50,7 @@ export function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end: thickEnd,
                 refName,
@@ -61,6 +64,7 @@ export function generateUcscTranscript(data) {
         else if (thickStart <= start && thickEnd > start && thickEnd < end) {
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end: thickEnd,
                 refName,

package/esm/index.js

@@ -1,11 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 import BedAdapterF from './BedAdapter';
 import BedGraphAdapterF from './BedGraphAdapter';
 import BedGraphTabixAdapterF from './BedGraphTabixAdapter';
 import BedTabixAdapterF from './BedTabixAdapter';
 import BedpeAdapterF from './BedpeAdapter';
 import BigBedAdapterF from './BigBedAdapter';
+import GuessAdapterF from './GuessAdapter';
 export default class BedPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -18,73 +18,6 @@ export default class BedPlugin extends Plugin {
         BedTabixAdapterF(pluginManager);
         BedGraphAdapterF(pluginManager);
         BedGraphTabixAdapterF(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.(bb|bigbed)$/i;
-                const adapterName = 'BigBedAdapter';
-                const fileName = getFileName(file);
-                const obj = {
-                    type: adapterName,
-                    bigBedLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bedpe(\.gz)?$/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$/i;
-                const adapterName = 'BedTabixAdapter';
-                const fileName = getFileName(file);
-                const indexName = index && getFileName(index);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedGzLocation: file,
-                        index: {
-                            location: index || makeIndex(file, '.tbi'),
-                            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-                        },
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bed$/i;
-                const adapterName = 'BedAdapter';
-                const fileName = getFileName(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => adapterName === 'BedpeAdapter'
-            ? 'VariantTrack'
-            : trackTypeGuesser(adapterName));
+        GuessAdapterF(pluginManager);
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,10 +37,10 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^5.0.0",
+    "@gmod/bbi": "^6.0.0",
     "@gmod/bed": "^2.1.2",
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/tabix": "^1.5.6"
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/tabix": "^2.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }