@jbrowse/plugin-bed 2.1.0 → 2.1.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BedAdapter/BedAdapter.js +122 -259
- package/dist/BedAdapter/BedAdapter.js.map +1 -1
- package/dist/BedAdapter/configSchema.js +1 -1
- package/dist/BedAdapter/configSchema.js.map +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js +61 -146
- package/dist/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/dist/BedTabixAdapter/configSchema.js +2 -2
- package/dist/BedTabixAdapter/configSchema.js.map +1 -1
- package/dist/BigBedAdapter/BigBedAdapter.js +95 -219
- package/dist/BigBedAdapter/BigBedAdapter.js.map +1 -1
- package/dist/BigBedAdapter/configSchema.js +1 -1
- package/dist/BigBedAdapter/configSchema.js.map +1 -1
- package/dist/index.js +45 -75
- package/dist/index.js.map +1 -1
- package/dist/util.js +62 -67
- package/dist/util.js.map +1 -1
- package/package.json +2 -3
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@@ -1,6 +1,6 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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const configuration_1 = require("@jbrowse/core/configuration");
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exports.default = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
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bigBedLocation: {
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type: 'fileLocation',
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@@ -1 +1 @@
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
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package/dist/index.js
CHANGED
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@@ -1,19 +1,4 @@
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"use strict";
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var __extends = (this && this.__extends) || (function () {
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var extendStatics = function (d, b) {
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extendStatics = Object.setPrototypeOf ||
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({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
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function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
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return extendStatics(d, b);
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};
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return function (d, b) {
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if (typeof b !== "function" && b !== null)
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throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
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extendStatics(d, b);
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function __() { this.constructor = d; }
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d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
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};
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})();
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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var desc = Object.getOwnPropertyDescriptor(m, k);
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@@ -41,35 +26,29 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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_this.name = 'BedPlugin';
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return _this;
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const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
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const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
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const BigBedAdapter_1 = require("./BigBedAdapter");
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const BedTabixAdapter_1 = require("./BedTabixAdapter");
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const BedAdapter_1 = require("./BedAdapter");
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const tracks_1 = require("@jbrowse/core/util/tracks");
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class BedPlugin extends Plugin_1.default {
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constructor() {
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super(...arguments);
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this.name = 'BedPlugin';
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}
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pluginManager.addAdapterType(
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var regexGuess = /\.(bb|bigbed)$/i;
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var adapterName = 'BigBedAdapter';
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var fileName = (0, tracks_1.getFileName)(file);
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var obj = {
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install(pluginManager) {
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pluginManager.addAdapterType(() => new AdapterType_1.default({
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name: 'BigBedAdapter',
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configSchema: BigBedAdapter_1.configSchema,
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getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter/BigBedAdapter'))).then(r => r.default),
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}));
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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return (file, index, adapterHint) => {
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const regexGuess = /\.(bb|bigbed)$/i;
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const adapterName = 'BigBedAdapter';
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const fileName = (0, tracks_1.getFileName)(file);
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const obj = {
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type: adapterName,
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bigBedLocation: file,
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};
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@@ -82,30 +61,22 @@ var BedPlugin = /** @class */ (function (_super) {
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return adapterGuesser(file, index, adapterHint);
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};
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});
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pluginManager.addAdapterType(
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});
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});
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
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return function (file, index, adapterHint) {
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var regexGuess = /\.bed\.b?gz$/i;
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var adapterName = 'BedTabixAdapter';
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var fileName = (0, tracks_1.getFileName)(file);
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var indexName = index && (0, tracks_1.getFileName)(index);
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pluginManager.addAdapterType(() => new AdapterType_1.default({
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name: 'BedTabixAdapter',
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configSchema: BedTabixAdapter_1.configSchema,
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getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter/BedTabixAdapter'))).then(r => r.default),
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}));
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pluginManager.addAdapterType(() => new AdapterType_1.default({
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name: 'BedAdapter',
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configSchema: BedAdapter_1.configSchema,
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getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter/BedAdapter'))).then(r => r.default),
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}));
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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return (file, index, adapterHint) => {
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const regexGuess = /\.bed\.b?gz$/i;
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const adapterName = 'BedTabixAdapter';
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const fileName = (0, tracks_1.getFileName)(file);
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const indexName = index && (0, tracks_1.getFileName)(index);
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if (regexGuess.test(fileName) || adapterHint === adapterName) {
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return {
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type: adapterName,
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@@ -119,11 +90,11 @@ var BedPlugin = /** @class */ (function (_super) {
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return adapterGuesser(file, index, adapterHint);
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};
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});
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation',
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return
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pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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return (file, index, adapterHint) => {
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const regexGuess = /\.bed$/i;
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const adapterName = 'BedAdapter';
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const fileName = (0, tracks_1.getFileName)(file);
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if (regexGuess.test(fileName) || adapterHint === adapterName) {
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return {
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type: adapterName,
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@@ -133,8 +104,7 @@ var BedPlugin = /** @class */ (function (_super) {
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return adapterGuesser(file, index, adapterHint);
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});
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}
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}(Plugin_1.default));
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}
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}
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exports.default = BedPlugin;
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//# sourceMappingURL=index.js.map
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kGAAyE;AACzE,kEAAyC;AAEzC,mDAA2E;AAC3E,uDAA+E;AAC/E,6CAAqE;AAErE,sDAKkC;AAElC,MAAqB,SAAU,SAAQ,gBAAM;IAA7C;;QACE,SAAI,GAAG,WAAW,CAAA;IA0GpB,CAAC;IAxGC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,YAAY,EAAE,4BAAyB;YACvC,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,+BAA+B,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC/D,CAAC,CACL,CAAA;QACD,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,IAAA,oBAAW,EAAC,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,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,iBAAiB;YACvB,YAAY,EAAE,8BAA2B;YACzC,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,mCAAmC,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CACL,CAAA;QAED,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,yBAAsB;YACpC,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,yBAAyB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACzD,CAAC,CACL,CAAA;QACD,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,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,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,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,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,IAAA,oBAAW,EAAC,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;AA3GD,4BA2GC"}
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const util_1 = require("@jbrowse/core/util");
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.filter(child => child.get('type') === 'block')
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.sort((a, b) => a.get('start') - b.get('start'))
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// left-side UTR
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const prime = feature.get('strand') > 0 ? 'five' : 'three';
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type: `${prime}_prime_UTR`,
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start,
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end,
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else if (thickStart > start && thickStart < end && thickEnd >= end) {
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44
33
|
// UTR | CDS
|
|
45
|
-
|
|
34
|
+
const prime = feature.get('strand') > 0 ? 'five' : 'three';
|
|
46
35
|
newChildren.push({
|
|
47
|
-
type:
|
|
48
|
-
start
|
|
36
|
+
type: `${prime}_prime_UTR`,
|
|
37
|
+
start,
|
|
49
38
|
end: thickStart,
|
|
50
39
|
}, {
|
|
51
40
|
type: 'CDS',
|
|
52
41
|
start: thickStart,
|
|
53
|
-
end
|
|
42
|
+
end,
|
|
54
43
|
});
|
|
55
44
|
}
|
|
56
45
|
else if (thickStart <= start && thickEnd >= end) {
|
|
57
46
|
// CDS
|
|
58
47
|
newChildren.push({
|
|
59
48
|
type: 'CDS',
|
|
60
|
-
start
|
|
61
|
-
end
|
|
49
|
+
start,
|
|
50
|
+
end,
|
|
62
51
|
});
|
|
63
52
|
}
|
|
64
53
|
else if (thickStart > start && thickStart < end && thickEnd < end) {
|
|
65
54
|
// UTR | CDS | UTR
|
|
66
|
-
|
|
67
|
-
|
|
55
|
+
const leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
|
|
56
|
+
const rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
|
|
68
57
|
newChildren.push({
|
|
69
|
-
type:
|
|
70
|
-
start
|
|
58
|
+
type: `${leftPrime}_prime_UTR`,
|
|
59
|
+
start,
|
|
71
60
|
end: thickStart,
|
|
72
61
|
}, {
|
|
73
|
-
type:
|
|
62
|
+
type: `CDS`,
|
|
74
63
|
start: thickStart,
|
|
75
64
|
end: thickEnd,
|
|
76
65
|
}, {
|
|
77
|
-
type:
|
|
66
|
+
type: `${rightPrime}_prime_UTR`,
|
|
78
67
|
start: thickEnd,
|
|
79
|
-
end
|
|
68
|
+
end,
|
|
80
69
|
});
|
|
81
70
|
}
|
|
82
71
|
else if (thickStart <= start && thickEnd > start && thickEnd < end) {
|
|
83
72
|
// CDS | UTR
|
|
84
|
-
|
|
73
|
+
const prime = feature.get('strand') > 0 ? 'three' : 'five';
|
|
85
74
|
newChildren.push({
|
|
86
|
-
type:
|
|
87
|
-
start
|
|
75
|
+
type: `CDS`,
|
|
76
|
+
start,
|
|
88
77
|
end: thickEnd,
|
|
89
78
|
}, {
|
|
90
|
-
type:
|
|
79
|
+
type: `${prime}_prime_UTR`,
|
|
91
80
|
start: thickEnd,
|
|
92
|
-
end
|
|
81
|
+
end,
|
|
93
82
|
});
|
|
94
83
|
}
|
|
95
84
|
else if (thickEnd <= start) {
|
|
96
85
|
// right-side UTR
|
|
97
|
-
|
|
86
|
+
const prime = feature.get('strand') > 0 ? 'three' : 'five';
|
|
98
87
|
newChildren.push({
|
|
99
|
-
type:
|
|
100
|
-
start
|
|
101
|
-
end
|
|
88
|
+
type: `${prime}_prime_UTR`,
|
|
89
|
+
start,
|
|
90
|
+
end,
|
|
102
91
|
});
|
|
103
92
|
}
|
|
104
93
|
});
|
|
105
|
-
|
|
94
|
+
const newData = Object.fromEntries(feature.tags().map(tag => [tag, feature.get(tag)]));
|
|
106
95
|
newData.subfeatures = newChildren;
|
|
107
96
|
newData.type = 'mRNA';
|
|
108
97
|
newData.uniqueId = feature.id();
|
|
@@ -115,7 +104,7 @@ function ucscProcessedTranscript(feature) {
|
|
|
115
104
|
delete newData.blockCount;
|
|
116
105
|
delete newData.thickStart;
|
|
117
106
|
delete newData.thickEnd;
|
|
118
|
-
|
|
107
|
+
const newFeature = new util_1.SimpleFeature({
|
|
119
108
|
data: newData,
|
|
120
109
|
id: feature.id(),
|
|
121
110
|
});
|
|
@@ -123,28 +112,28 @@ function ucscProcessedTranscript(feature) {
|
|
|
123
112
|
}
|
|
124
113
|
exports.ucscProcessedTranscript = ucscProcessedTranscript;
|
|
125
114
|
function defaultParser(fields, line) {
|
|
126
|
-
return Object.fromEntries(line.split('\t').map(
|
|
115
|
+
return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
|
|
127
116
|
}
|
|
128
117
|
function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
118
|
+
const l = line.split('\t');
|
|
119
|
+
const refName = l[colRef];
|
|
120
|
+
const start = +l[colStart];
|
|
121
|
+
const colSame = colStart === colEnd ? 1 : 0;
|
|
122
|
+
const end = +l[colEnd] + colSame;
|
|
123
|
+
const data = names
|
|
135
124
|
? defaultParser(names, line)
|
|
136
|
-
: parser.parseLine(line, { uniqueId
|
|
137
|
-
|
|
125
|
+
: parser.parseLine(line, { uniqueId });
|
|
126
|
+
const { blockCount, blockSizes, blockStarts, chromStarts } = data;
|
|
138
127
|
if (blockCount) {
|
|
139
|
-
|
|
140
|
-
|
|
141
|
-
|
|
128
|
+
const starts = chromStarts || blockStarts || [];
|
|
129
|
+
const sizes = blockSizes;
|
|
130
|
+
const blocksOffset = start;
|
|
142
131
|
data.subfeatures = [];
|
|
143
|
-
for (
|
|
144
|
-
|
|
145
|
-
|
|
132
|
+
for (let b = 0; b < blockCount; b += 1) {
|
|
133
|
+
const bmin = (starts[b] || 0) + blocksOffset;
|
|
134
|
+
const bmax = bmin + (sizes[b] || 0);
|
|
146
135
|
data.subfeatures.push({
|
|
147
|
-
uniqueId:
|
|
136
|
+
uniqueId: `${uniqueId}-${b}`,
|
|
148
137
|
start: bmin,
|
|
149
138
|
end: bmax,
|
|
150
139
|
type: 'block',
|
|
@@ -157,7 +146,13 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
|
|
|
157
146
|
delete data.chrom;
|
|
158
147
|
delete data.chromStart;
|
|
159
148
|
delete data.chromEnd;
|
|
160
|
-
|
|
149
|
+
const f = new util_1.SimpleFeature({
|
|
150
|
+
...data,
|
|
151
|
+
start,
|
|
152
|
+
end,
|
|
153
|
+
refName,
|
|
154
|
+
uniqueId,
|
|
155
|
+
});
|
|
161
156
|
return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
|
|
162
157
|
}
|
|
163
158
|
exports.featureData = featureData;
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAAA,6CAA2D;AAG3D,SAAgB,uBAAuB,CAAC,OAAgB;IACtD,MAAM,QAAQ,GAAG,OAAO,CAAC,QAAQ,EAAE,CAAA;IACnC,4CAA4C;IAC5C,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAC5C,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;IAExC,IAAI,CAAC,UAAU,IAAI,CAAC,QAAQ,EAAE;QAC5B,OAAO,OAAO,CAAA;KACf;IAED,MAAM,MAAM,GAAc,QAAQ;QAChC,CAAC,CAAC,QAAQ;aACL,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,OAAO,CAAC;aAC9C,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QACpD,CAAC,CAAC,EAAE,CAAA;IAEN,8DAA8D;IAC9D,MAAM,WAAW,GAAwB,EAAE,CAAA;IAC3C,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAChC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC5B,IAAI,UAAU,IAAI,GAAG,EAAE;YACrB,gBAAgB;YAChB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC1D,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;aAAM,IAAI,UAAU,GAAG,KAAK,IAAI,UAAU,GAAG,GAAG,IAAI,QAAQ,IAAI,GAAG,EAAE;YACpE,YAAY;YACZ,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC1D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG,EAAE,UAAU;aAChB,EACD;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK,EAAE,UAAU;gBACjB,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,UAAU,IAAI,KAAK,IAAI,QAAQ,IAAI,GAAG,EAAE;YACjD,MAAM;YACN,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,KAAK;gBACX,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;aAAM,IAAI,UAAU,GAAG,KAAK,IAAI,UAAU,GAAG,GAAG,IAAI,QAAQ,GAAG,GAAG,EAAE;YACnE,kBAAkB;YAClB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAA;YAC9D,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC/D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,GAAG,SAAS,YAAY;gBAC9B,KAAK;gBACL,GAAG,EAAE,UAAU;aAChB,EACD;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK,EAAE,UAAU;gBACjB,GAAG,EAAE,QAAQ;aACd,EACD;gBACE,IAAI,EAAE,GAAG,UAAU,YAAY;gBAC/B,KAAK,EAAE,QAAQ;gBACf,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,UAAU,IAAI,KAAK,IAAI,QAAQ,GAAG,KAAK,IAAI,QAAQ,GAAG,GAAG,EAAE;YACpE,YAAY;YACZ,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC1D,WAAW,CAAC,IAAI,CACd;gBACE,IAAI,EAAE,KAAK;gBACX,KAAK;gBACL,GAAG,EAAE,QAAQ;aACd,EACD;gBACE,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK,EAAE,QAAQ;gBACf,GAAG;aACJ,CACF,CAAA;SACF;aAAM,IAAI,QAAQ,IAAI,KAAK,EAAE;YAC5B,iBAAiB;YACjB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;YAC1D,WAAW,CAAC,IAAI,CAAC;gBACf,IAAI,EAAE,GAAG,KAAK,YAAY;gBAC1B,KAAK;gBACL,GAAG;aACJ,CAAC,CAAA;SACH;IACH,CAAC,CAAC,CAAA;IACF,MAAM,OAAO,GAAG,MAAM,CAAC,WAAW,CAChC,OAAO,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CACnD,CAAA;IACD,OAAO,CAAC,WAAW,GAAG,WAAW,CAAA;IACjC,OAAO,CAAC,IAAI,GAAG,MAAM,CAAA;IACrB,OAAO,CAAC,QAAQ,GAAG,OAAO,CAAC,EAAE,EAAE,CAAA;IAC/B,OAAO,OAAO,CAAC,WAAW,CAAA;IAC1B,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,QAAQ,CAAA;IACvB,OAAO,OAAO,CAAC,KAAK,CAAA;IACpB,OAAO,OAAO,CAAC,WAAW,CAAA;IAC1B,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,UAAU,CAAA;IACzB,OAAO,OAAO,CAAC,QAAQ,CAAA;IACvB,MAAM,UAAU,GAAG,IAAI,oBAAa,CAAC;QACnC,IAAI,EAAE,OAAO;QACb,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;KACjB,CAAC,CAAA;IACF,OAAO,UAAU,CAAA;AACnB,CAAC;AArHD,0DAqHC;AAED,SAAS,aAAa,CAAC,MAAgB,EAAE,IAAY;IACnD,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;AAC3E,CAAC;AAED,SAAgB,WAAW,CACzB,IAAY,EACZ,MAAc,EACd,QAAgB,EAChB,MAAc,EACd,WAAmB,EACnB,MAAW,EACX,QAAgB,EAChB,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,OAAO,GAAG,CAAC,CAAC,MAAM,CAAC,CAAA;IACzB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;IAC1B,MAAM,OAAO,GAAG,QAAQ,KAAK,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE3C,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;IAChC,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,aAAa,CAAC,KAAK,EAAE,IAAI,CAAC;QAC5B,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAA;IAExC,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;IAEjE,IAAI,UAAU,EAAE;QACd,MAAM,MAAM,GAAG,WAAW,IAAI,WAAW,IAAI,EAAE,CAAA;QAC/C,MAAM,KAAK,GAAG,UAAU,CAAA;QACxB,MAAM,YAAY,GAAG,KAAK,CAAA;QAC1B,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;QAErB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;YACtC,MAAM,IAAI,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;YAC5C,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;YACnC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;gBACpB,QAAQ,EAAE,GAAG,QAAQ,IAAI,CAAC,EAAE;gBAC5B,KAAK,EAAE,IAAI;gBACX,GAAG,EAAE,IAAI;gBACT,IAAI,EAAE,OAAO;aACd,CAAC,CAAA;SACH;KACF;IAED,IAAI,WAAW,EAAE;QACf,IAAI,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;KAChC;IACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACjB,OAAO,IAAI,CAAC,UAAU,CAAA;IACtB,OAAO,IAAI,CAAC,QAAQ,CAAA;IACpB,MAAM,CAAC,GAAG,IAAI,oBAAa,CAAC;QAC1B,GAAG,IAAI;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,QAAQ;KACT,CAAC,CAAA;IACF,OAAO,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7D,CAAC;AAtDD,kCAsDC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.3",
|
|
4
4
|
"description": "JBrowse 2 bed adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -37,7 +37,6 @@
|
|
|
37
37
|
"clean": "rimraf dist esm *.tsbuildinfo"
|
|
38
38
|
},
|
|
39
39
|
"dependencies": {
|
|
40
|
-
"@babel/runtime": "^7.17.9",
|
|
41
40
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
42
41
|
"@gmod/bbi": "^2.0.2",
|
|
43
42
|
"@gmod/bed": "^2.1.2",
|
|
@@ -57,5 +56,5 @@
|
|
|
57
56
|
"distModule": "esm/index.js",
|
|
58
57
|
"srcModule": "src/index.ts",
|
|
59
58
|
"module": "esm/index.js",
|
|
60
|
-
"gitHead": "
|
|
59
|
+
"gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
|
|
61
60
|
}
|