@jbrowse/plugin-variants 1.7.0 → 1.7.4

package/dist/VcfAdapter/VcfAdapter.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -43,7 +43,7 @@ var _vcf = _interopRequireDefault(require("@gmod/vcf"));
 
 var _VcfFeature = _interopRequireDefault(require("../VcfTabixAdapter/VcfFeature"));
 
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
@@ -69,31 +69,31 @@ function isGzip(buf) {
 }
 
 var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(VcfAdapter, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(VcfAdapter, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(VcfAdapter);
 
   function VcfAdapter() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, VcfAdapter);
+    (0, _classCallCheck2.default)(this, VcfAdapter);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "vcfFeatures", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "vcfFeatures", void 0);
     return _this;
   }
 
-  (0, _createClass2["default"])(VcfAdapter, [{
+  (0, _createClass2.default)(VcfAdapter, [{
     key: "getHeader",
     value: function () {
-      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var _yield$this$setup, header;
 
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -122,10 +122,10 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getMetadata",
     value: function () {
-      var _getMetadata = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
         var _yield$this$setup2, header, parser;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -135,7 +135,7 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
               case 2:
                 _yield$this$setup2 = _context2.sent;
                 header = _yield$this$setup2.header;
-                parser = new _vcf["default"]({
+                parser = new _vcf.default({
                   header: header
                 });
                 return _context2.abrupt("return", parser.getMetadata());
@@ -158,10 +158,10 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setupP",
     value: function () {
-      var _setupP = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+      var _setupP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
         var buffer, buf, str, _readVcf, header, lines, intervalTree;
 
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -204,7 +204,7 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   var _info$match;
 
                   var _line$split = line.split('\t'),
-                      _line$split2 = (0, _slicedToArray2["default"])(_line$split, 8),
+                      _line$split2 = (0, _slicedToArray2.default)(_line$split, 8),
                       refName = _line$split2[0],
                       startP = _line$split2[1],
                       ref = _line$split2[3],
@@ -223,7 +223,7 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   var key = obj.refName;
 
                   if (!acc[key]) {
-                    acc[key] = new _intervalTree["default"]();
+                    acc[key] = new _intervalTree.default();
                   }
 
                   acc[key].insert([obj.start, obj.end], obj);
@@ -251,15 +251,15 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setup",
     value: function () {
-      var _setup = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
         var _this2 = this;
 
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
                 if (!this.vcfFeatures) {
-                  this.vcfFeatures = this.setupP()["catch"](function (e) {
+                  this.vcfFeatures = this.setupP().catch(function (e) {
                     _this2.vcfFeatures = undefined;
                     throw e;
                   });
@@ -284,13 +284,13 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
         var _,
             _yield$this$setup3,
             intervalTree,
             _args5 = arguments;
 
-        return _regenerator["default"].wrap(function _callee5$(_context5) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
@@ -324,10 +324,10 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(observer) {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(observer) {
           var _intervalTree$refName, start, end, refName, _yield$_this3$setup, header, intervalTree, parser;
 
-          return _regenerator["default"].wrap(function _callee6$(_context6) {
+          return _regenerator.default.wrap(function _callee6$(_context6) {
             while (1) {
               switch (_context6.prev = _context6.next) {
                 case 0:
@@ -340,11 +340,11 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   _yield$_this3$setup = _context6.sent;
                   header = _yield$_this3$setup.header;
                   intervalTree = _yield$_this3$setup.intervalTree;
-                  parser = new _vcf["default"]({
+                  parser = new _vcf.default({
                     header: header
                   });
                   (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
-                    return observer.next(new _VcfFeature["default"]({
+                    return observer.next(new _VcfFeature.default({
                       variant: parser.parseLine(f.line),
                       parser: parser,
                       id: "".concat(_this3.id, "-").concat(f.id)
@@ -379,5 +379,5 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   return VcfAdapter;
 }(_BaseAdapter.BaseFeatureDataAdapter);
 
-exports["default"] = VcfAdapter;
-(0, _defineProperty2["default"])(VcfAdapter, "capabilities", ['getFeatures', 'getRefNames']);
+exports.default = VcfAdapter;
+(0, _defineProperty2.default)(VcfAdapter, "capabilities", ['getFeatures', 'getRefNames']);

package/dist/VcfAdapter/VcfAdapter.test.js

@@ -15,13 +15,13 @@ var _configSchema = _interopRequireDefault(require("./configSchema"));
 var _webEncoding = require("web-encoding");
 
 window.TextDecoder = _webEncoding.TextDecoder;
-test('adapter can fetch variants from volvox.vcf', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+test('adapter can fetch variants from volvox.vcf', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
   var adapter, features, names, featuresArray;
-  return _regenerator["default"].wrap(function _callee$(_context) {
+  return _regenerator.default.wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
-          adapter = new _VcfAdapter["default"](_configSchema["default"].create({
+          adapter = new _VcfAdapter.default(_configSchema.default.create({
             vcfLocation: {
               localPath: require.resolve('./test_data/volvox.filtered.vcf'),
               locationType: 'LocalPathLocation'

package/dist/VcfAdapter/configSchema.d.ts

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

package/dist/VcfAdapter/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -19,4 +19,4 @@ var _default = (0, _configuration.ConfigurationSchema)('VcfAdapter', {
   explicitlyTyped: true
 });
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/VcfAdapter/index.d.ts

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

package/dist/VcfAdapter/index.js

@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", {
 Object.defineProperty(exports, "configSchema", {
   enumerable: true,
   get: function get() {
-    return _configSchema["default"];
+    return _configSchema.default;
   }
 });
 

package/dist/VcfTabixAdapter/VcfFeature.d.ts

@@ -1,59 +1,59 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-/**
- * VCF Feature creation with lazy genotype evaluation.
- */
-interface Samples {
-    [key: string]: {
-        [key: string]: {
-            values: string[] | number[] | null;
-        };
-    };
-}
-interface FeatureData {
-    [key: string]: unknown;
-    refName: string;
-    start: number;
-    end: number;
-    description?: string;
-    type?: string;
-    name?: string;
-    aliases?: string[];
-    samples?: Samples;
-}
-export default class VCFFeature implements Feature {
-    private variant;
-    private parser;
-    private data;
-    private _id;
-    constructor(args: {
-        variant: any;
-        parser: any;
-        id: string;
-    });
-    get(field: string): any;
-    set(): void;
-    parent(): undefined;
-    children(): undefined;
-    tags(): string[];
-    id(): string;
-    dataFromVariant(variant: {
-        REF: string;
-        POS: number;
-        ALT: string[];
-        CHROM: string;
-        INFO: any;
-        ID: string[];
-    }): FeatureData;
-    /**
-     * Get a sequence ontology (SO) term that describes the variant type
-     */
-    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
-    static _altTypeToSO: {
-        [key: string]: string | undefined;
-    };
-    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
-    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
-    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
-    toJSON(): any;
-}
-export {};
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+/**
+ * VCF Feature creation with lazy genotype evaluation.
+ */
+interface Samples {
+    [key: string]: {
+        [key: string]: {
+            values: string[] | number[] | null;
+        };
+    };
+}
+interface FeatureData {
+    [key: string]: unknown;
+    refName: string;
+    start: number;
+    end: number;
+    description?: string;
+    type?: string;
+    name?: string;
+    aliases?: string[];
+    samples?: Samples;
+}
+export default class VCFFeature implements Feature {
+    private variant;
+    private parser;
+    private data;
+    private _id;
+    constructor(args: {
+        variant: any;
+        parser: any;
+        id: string;
+    });
+    get(field: string): any;
+    set(): void;
+    parent(): undefined;
+    children(): undefined;
+    tags(): string[];
+    id(): string;
+    dataFromVariant(variant: {
+        REF: string;
+        POS: number;
+        ALT: string[];
+        CHROM: string;
+        INFO: any;
+        ID: string[];
+    }): FeatureData;
+    /**
+     * Get a sequence ontology (SO) term that describes the variant type
+     */
+    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
+    static _altTypeToSO: {
+        [key: string]: string | undefined;
+    };
+    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
+    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
+    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
+    toJSON(): any;
+}
+export {};

package/dist/VcfTabixAdapter/VcfFeature.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
@@ -21,18 +21,18 @@ var _vcf = require("@gmod/vcf");
 
 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; }
+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 VCFFeature = /*#__PURE__*/function () {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   function VCFFeature(args) {
-    (0, _classCallCheck2["default"])(this, VCFFeature);
-    (0, _defineProperty2["default"])(this, "variant", void 0);
-    (0, _defineProperty2["default"])(this, "parser", void 0);
-    (0, _defineProperty2["default"])(this, "data", void 0);
-    (0, _defineProperty2["default"])(this, "_id", void 0);
+    (0, _classCallCheck2.default)(this, VCFFeature);
+    (0, _defineProperty2.default)(this, "variant", void 0);
+    (0, _defineProperty2.default)(this, "parser", void 0);
+    (0, _defineProperty2.default)(this, "data", void 0);
+    (0, _defineProperty2.default)(this, "_id", void 0);
     this.variant = args.variant;
     this.parser = args.parser;
     this.data = this.dataFromVariant(this.variant);
@@ -40,7 +40,7 @@ var VCFFeature = /*#__PURE__*/function () {
   } // eslint-disable-next-line @typescript-eslint/no-explicit-any
 
 
-  (0, _createClass2["default"])(VCFFeature, [{
+  (0, _createClass2.default)(VCFFeature, [{
     key: "get",
     value: function get(field) {
       return field === 'samples' ? this.variant.SAMPLES : this.data[field] || this.variant[field];
@@ -61,7 +61,7 @@ var VCFFeature = /*#__PURE__*/function () {
   }, {
     key: "tags",
     value: function tags() {
-      var t = [].concat((0, _toConsumableArray2["default"])(Object.keys(this.data)), (0, _toConsumableArray2["default"])(Object.keys(this.variant)), ['samples']);
+      var t = [].concat((0, _toConsumableArray2.default)(Object.keys(this.data)), (0, _toConsumableArray2.default)(Object.keys(this.variant)), ['samples']);
       return t;
     }
   }, {
@@ -81,7 +81,7 @@ var VCFFeature = /*#__PURE__*/function () {
       var start = POS - 1;
 
       var _this$_getSOTermAndDe = this._getSOTermAndDescription(REF, ALT),
-          _this$_getSOTermAndDe2 = (0, _slicedToArray2["default"])(_this$_getSOTermAndDe, 2),
+          _this$_getSOTermAndDe2 = (0, _slicedToArray2.default)(_this$_getSOTermAndDe, 2),
           SO_term = _this$_getSOTermAndDe2[0],
           description = _this$_getSOTermAndDe2[1];
 
@@ -119,7 +119,7 @@ var VCFFeature = /*#__PURE__*/function () {
       var descriptions = new Set();
       alt.forEach(function (a) {
         var _this$_getSOAndDescFr = _this._getSOAndDescFromAltDefs(ref, a),
-            _this$_getSOAndDescFr2 = (0, _slicedToArray2["default"])(_this$_getSOAndDescFr, 2),
+            _this$_getSOAndDescFr2 = (0, _slicedToArray2.default)(_this$_getSOAndDescFr, 2),
             soTerm = _this$_getSOAndDescFr2[0],
             description = _this$_getSOAndDescFr2[1];
 
@@ -128,7 +128,7 @@ var VCFFeature = /*#__PURE__*/function () {
 
           var _this$_getSOAndDescBy = _this._getSOAndDescByExamination(ref, a);
 
-          var _this$_getSOAndDescBy2 = (0, _slicedToArray2["default"])(_this$_getSOAndDescBy, 2);
+          var _this$_getSOAndDescBy2 = (0, _slicedToArray2.default)(_this$_getSOAndDescBy, 2);
 
           soTerm = _this$_getSOAndDescBy2[0];
           description = _this$_getSOAndDescBy2[1];
@@ -141,24 +141,24 @@ var VCFFeature = /*#__PURE__*/function () {
       }); // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
 
       if (descriptions.size > 1) {
-        var prefixes = new Set((0, _toConsumableArray2["default"])(descriptions).map(function (desc) {
+        var prefixes = new Set((0, _toConsumableArray2.default)(descriptions).map(function (desc) {
           var prefix = desc.split('->');
           return prefix[1] ? prefix[0] : desc;
         }));
-        var new_descs = (0, _toConsumableArray2["default"])(prefixes).map(function (prefix) {
-          var suffixes = (0, _toConsumableArray2["default"])(descriptions).map(function (desc) {
+        var new_descs = (0, _toConsumableArray2.default)(prefixes).map(function (prefix) {
+          var suffixes = (0, _toConsumableArray2.default)(descriptions).map(function (desc) {
             var pref = desc.split('-> ');
             return pref[1] && pref[0] === prefix ? pref[1] : '';
           }).filter(function (f) {
             return !!f;
           });
-          return suffixes.length ? prefix + '-> ' + suffixes.join(',') : (0, _toConsumableArray2["default"])(descriptions).join(',');
+          return suffixes.length ? prefix + '-> ' + suffixes.join(',') : (0, _toConsumableArray2.default)(descriptions).join(',');
         });
         descriptions = new Set(new_descs);
       }
 
       if (soTerms.size) {
-        return [(0, _toConsumableArray2["default"])(soTerms).join(','), (0, _toConsumableArray2["default"])(descriptions).join(',')];
+        return [(0, _toConsumableArray2.default)(soTerms).join(','), (0, _toConsumableArray2.default)(descriptions).join(',')];
       }
 
       return [undefined, undefined];
@@ -246,8 +246,8 @@ var VCFFeature = /*#__PURE__*/function () {
   return VCFFeature;
 }();
 
-exports["default"] = VCFFeature;
-(0, _defineProperty2["default"])(VCFFeature, "_altTypeToSO", {
+exports.default = VCFFeature;
+(0, _defineProperty2.default)(VCFFeature, "_altTypeToSO", {
   DEL: 'deletion',
   INS: 'insertion',
   DUP: 'duplication',

package/dist/VcfTabixAdapter/VcfFeature.test.js

@@ -7,12 +7,12 @@ var _vcf = _interopRequireDefault(require("@gmod/vcf"));
 var _VcfFeature = _interopRequireDefault(require("./VcfFeature"));
 
 test('test usage of the VcfFeature', function () {
-  var parser = new _vcf["default"]({
+  var parser = new _vcf.default({
     header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
   });
   var line = "lcl|Scaffald_1\t80465\trs118266897\tR\tA\t29\tPASS\tNS=3;0,14;AF=0.5;DB;112;PG2.1";
   var variant = parser.parseLine(line);
-  var f = new _VcfFeature["default"]({
+  var f = new _VcfFeature.default({
     parser: parser,
     variant: variant,
     id: 'myuniqueid'
@@ -21,12 +21,12 @@ test('test usage of the VcfFeature', function () {
   expect(f.get('name')).toEqual('rs118266897');
 });
 test('try INS feature with END less than start', function () {
-  var parser = new _vcf["default"]({
+  var parser = new _vcf.default({
     header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
   });
   var line = "chr1\t100\trs123\tR\tA\t29\tPASS\tEND=1;SVTYPE=INS";
   var variant = parser.parseLine(line);
-  var f = new _VcfFeature["default"]({
+  var f = new _VcfFeature.default({
     parser: parser,
     variant: variant,
     id: 'myuniqueid'
@@ -36,12 +36,12 @@ test('try INS feature with END less than start', function () {
   expect(f.get('end')).toEqual(100);
 });
 test('try DEL feature with END info field valid', function () {
-  var parser = new _vcf["default"]({
+  var parser = new _vcf.default({
     header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
   });
   var line = "chr1\t100\trs123\tR\t<DEL>\t29\tPASS\tEND=1000;SVTYPE=DEL";
   var variant = parser.parseLine(line);
-  var f = new _VcfFeature["default"]({
+  var f = new _VcfFeature.default({
     parser: parser,
     variant: variant,
     id: 'myuniqueid'
@@ -52,12 +52,12 @@ test('try DEL feature with END info field valid', function () {
 });
 describe('test SV description', function () {
   it('multiple SVs', function () {
-    var parser = new _vcf["default"]({
+    var parser = new _vcf.default({
       header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
     });
     var line = "chr1\t100\trs123\tR\t<INVDUP>,<INV>\t29\tPASS\tEND=1000;SVTYPE=DEL";
     var variant = parser.parseLine(line);
-    var f = new _VcfFeature["default"]({
+    var f = new _VcfFeature.default({
       parser: parser,
       variant: variant,
       id: 'myuniqueid'
@@ -65,12 +65,12 @@ describe('test SV description', function () {
     expect(f.get('description')).toEqual('<INVDUP>,<INV>');
   });
   it('BND', function () {
-    var parser = new _vcf["default"]({
+    var parser = new _vcf.default({
       header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
     });
     var line = "chr1\t100\trs123\tR\tG[ctgA:34200[\t29\tPASS\tEND=1000;SVTYPE=BND";
     var variant = parser.parseLine(line);
-    var f = new _VcfFeature["default"]({
+    var f = new _VcfFeature.default({
       parser: parser,
       variant: variant,
       id: 'myuniqueid'
@@ -78,12 +78,12 @@ describe('test SV description', function () {
     expect(f.get('description')).toEqual('G[ctgA:34200[');
   });
   it('multiple BND', function () {
-    var parser = new _vcf["default"]({
+    var parser = new _vcf.default({
       header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
     });
     var line = "chr1\t100\trs123\tR\tG[ctgA:34200[,G[ctgA:44200[\t29\tPASS\tEND=1000;SVTYPE=BND";
     var variant = parser.parseLine(line);
-    var f = new _VcfFeature["default"]({
+    var f = new _VcfFeature.default({
       parser: parser,
       variant: variant,
       id: 'myuniqueid'
@@ -91,12 +91,12 @@ describe('test SV description', function () {
     expect(f.get('description')).toEqual('G[ctgA:34200[,G[ctgA:44200[');
   });
   it('multiple SNV', function () {
-    var parser = new _vcf["default"]({
+    var parser = new _vcf.default({
       header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
     });
     var line = "chr1\t100\trs123\tG\tA,C\t29\tPASS\tHELLO=world";
     var variant = parser.parseLine(line);
-    var f = new _VcfFeature["default"]({
+    var f = new _VcfFeature.default({
       parser: parser,
       variant: variant,
       id: 'myuniqueid'

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,35 +1,35 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { TabixIndexedFile } from '@gmod/tabix';
-import VcfParser from '@gmod/vcf';
-import { GenericFilehandle } from 'generic-filehandle';
-export default class extends BaseFeatureDataAdapter {
-    private configured?;
-    private configurePre;
-    protected configure(): Promise<{
-        filehandle: GenericFilehandle;
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<any>;
-    getHeader(): Promise<string>;
-    getMetadata(): Promise<any>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import VcfParser from '@gmod/vcf';
+import { GenericFilehandle } from 'generic-filehandle';
+export default class extends BaseFeatureDataAdapter {
+    private configured?;
+    private configurePre;
+    protected configure(): Promise<{
+        filehandle: GenericFilehandle;
+        vcf: TabixIndexedFile;
+        parser: VcfParser;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getMetadata(): Promise<any>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * Checks if the data source has data for the given reference sequence,
+     * and then gets the features in the region if it does
+     *
+     * Currently this just calls getFeatureInRegion for each region. Adapters that
+     * are frequently called on multiple regions simultaneously may want to
+     * implement a more efficient custom version of this method.
+     *
+     * Also includes a bit of extra logging to warn when fetching a large portion
+     * of a VCF
+     * @param regions - Regions
+     * @param opts - Feature adapter options
+     * @returns Observable of Feature objects in the regions
+     */
+    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}