@jbrowse/plugin-variants 1.7.10 → 2.0.1

package/dist/VcfAdapter/configSchema.js

@@ -1,22 +1,10 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('VcfAdapter', {
-  vcfLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.vcf',
-      locationType: 'UriLocation'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
+    vcfLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/VcfAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/VcfAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/VcfAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/VcfTabixAdapter/VcfFeature.js

@@ -1,261 +1,218 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-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; }
-
-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);
-    this.variant = args.variant;
-    this.parser = args.parser;
-    this.data = this.dataFromVariant(this.variant);
-    this._id = args.id;
-  } // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
-  (0, _createClass2.default)(VCFFeature, [{
-    key: "get",
-    value: function get(field) {
-      return field === 'samples' ? this.variant.SAMPLES : this.data[field] || this.variant[field];
-    }
-  }, {
-    key: "set",
-    value: function set() {}
-  }, {
-    key: "parent",
-    value: function parent() {
-      return undefined;
-    }
-  }, {
-    key: "children",
-    value: function children() {
-      return undefined;
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
     }
-  }, {
-    key: "tags",
-    value: function tags() {
-      var t = [].concat((0, _toConsumableArray2.default)(Object.keys(this.data)), (0, _toConsumableArray2.default)(Object.keys(this.variant)), ['samples']);
-      return t;
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
     }
-  }, {
-    key: "id",
-    value: function id() {
-      return this._id;
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
     }
-  }, {
-    key: "dataFromVariant",
-    value: function dataFromVariant(variant) {
-      var REF = variant.REF,
-          ALT = variant.ALT,
-          POS = variant.POS,
-          CHROM = variant.CHROM,
-          INFO = variant.INFO,
-          ID = variant.ID;
-      var start = POS - 1;
-
-      var _this$_getSOTermAndDe = this._getSOTermAndDescription(REF, ALT),
-          _this$_getSOTermAndDe2 = (0, _slicedToArray2.default)(_this$_getSOTermAndDe, 2),
-          SO_term = _this$_getSOTermAndDe2[0],
-          description = _this$_getSOTermAndDe2[1];
-
-      var isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) {
-        return f === '<TRA>';
-      });
-      var isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) {
-        return f.indexOf('<') !== -1;
-      });
-      return {
-        refName: CHROM,
-        start: start,
-        end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-        description: description,
-        type: SO_term,
-        name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-        aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined
-      };
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var vcf_1 = require("@gmod/vcf");
+var VCFFeature = /** @class */ (function () {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    function VCFFeature(args) {
+        this.variant = args.variant;
+        this.parser = args.parser;
+        this.data = this.dataFromVariant(this.variant);
+        this._id = args.id;
     }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    VCFFeature.prototype.get = function (field) {
+        return field === 'samples'
+            ? this.variant.SAMPLES
+            : this.data[field] || this.variant[field];
+    };
+    VCFFeature.prototype.set = function () { };
+    VCFFeature.prototype.parent = function () {
+        return undefined;
+    };
+    VCFFeature.prototype.children = function () {
+        return undefined;
+    };
+    VCFFeature.prototype.tags = function () {
+        var t = __spreadArray(__spreadArray(__spreadArray([], __read(Object.keys(this.data)), false), __read(Object.keys(this.variant)), false), [
+            'samples',
+        ], false);
+        return t;
+    };
+    VCFFeature.prototype.id = function () {
+        return this._id;
+    };
+    VCFFeature.prototype.dataFromVariant = function (variant) {
+        var REF = variant.REF, ALT = variant.ALT, POS = variant.POS, CHROM = variant.CHROM, INFO = variant.INFO, ID = variant.ID;
+        var start = POS - 1;
+        var _a = __read(this._getSOTermAndDescription(REF, ALT), 2), SO_term = _a[0], description = _a[1];
+        var isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) { return f === '<TRA>'; });
+        var isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) { return f.indexOf('<') !== -1; });
+        return {
+            refName: CHROM,
+            start: start,
+            end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
+            description: description,
+            type: SO_term,
+            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+        };
+    };
     /**
      * Get a sequence ontology (SO) term that describes the variant type
      */
-
-  }, {
-    key: "_getSOTermAndDescription",
-    value: function _getSOTermAndDescription(ref, alt) {
-      var _this = this;
-
-      // it's just a remark if there are no alternate alleles
-      if (!alt || alt === []) {
-        return ['remark', 'no alternative alleles'];
-      }
-
-      var soTerms = new Set();
-      var descriptions = new Set();
-      alt.forEach(function (a) {
-        var _this$_getSOAndDescFr = _this._getSOAndDescFromAltDefs(ref, a),
-            _this$_getSOAndDescFr2 = (0, _slicedToArray2.default)(_this$_getSOAndDescFr, 2),
-            soTerm = _this$_getSOAndDescFr2[0],
-            description = _this$_getSOAndDescFr2[1];
-
-        if (!soTerm) {
-          ;
-
-          var _this$_getSOAndDescBy = _this._getSOAndDescByExamination(ref, a);
-
-          var _this$_getSOAndDescBy2 = (0, _slicedToArray2.default)(_this$_getSOAndDescBy, 2);
-
-          soTerm = _this$_getSOAndDescBy2[0];
-          description = _this$_getSOAndDescBy2[1];
-        }
-
-        if (soTerm && description) {
-          soTerms.add(soTerm);
-          descriptions.add(description);
+    VCFFeature.prototype._getSOTermAndDescription = function (ref, alt) {
+        var _this = this;
+        // it's just a remark if there are no alternate alleles
+        if (!alt || alt === []) {
+            return ['remark', 'no alternative alleles'];
         }
-      }); // 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 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 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(',');
+        var soTerms = new Set();
+        var descriptions = new Set();
+        alt.forEach(function (a) {
+            var _a;
+            var _b = __read(_this._getSOAndDescFromAltDefs(ref, a), 2), soTerm = _b[0], description = _b[1];
+            if (!soTerm) {
+                ;
+                _a = __read(_this._getSOAndDescByExamination(ref, a), 2), soTerm = _a[0], description = _a[1];
+            }
+            if (soTerm && description) {
+                soTerms.add(soTerm);
+                descriptions.add(description);
+            }
         });
-        descriptions = new Set(new_descs);
-      }
-
-      if (soTerms.size) {
-        return [(0, _toConsumableArray2.default)(soTerms).join(','), (0, _toConsumableArray2.default)(descriptions).join(',')];
-      }
-
-      return [undefined, undefined];
-    }
-  }, {
-    key: "_getSOAndDescFromAltDefs",
-    value: function _getSOAndDescFromAltDefs(ref, alt) {
-      if (typeof alt === 'string' && !alt.startsWith('<')) {
+        // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
+        if (descriptions.size > 1) {
+            var prefixes = new Set(__spreadArray([], __read(descriptions), false).map(function (desc) {
+                var prefix = desc.split('->');
+                return prefix[1] ? prefix[0] : desc;
+            }));
+            var new_descs = __spreadArray([], __read(prefixes), false).map(function (prefix) {
+                var suffixes = __spreadArray([], __read(descriptions), false).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(',')
+                    : __spreadArray([], __read(descriptions), false).join(',');
+            });
+            descriptions = new Set(new_descs);
+        }
+        if (soTerms.size) {
+            return [__spreadArray([], __read(soTerms), false).join(','), __spreadArray([], __read(descriptions), false).join(',')];
+        }
         return [undefined, undefined];
-      } // look for a definition with an SO type for this
-
-
-      var soTerm = VCFFeature._altTypeToSO[alt]; // if no SO term but ALT is in metadata, assume sequence_variant
-
-      if (!soTerm && this.parser.getMetadata('ALT', alt)) {
-        soTerm = 'sequence_variant';
-      }
-
-      if (soTerm) {
-        return [soTerm, alt];
-      } // try to look for a definition for a parent term if we can
-
-
-      var modAlt = alt.split(':');
-
-      if (modAlt.length > 1) {
-        return this._getSOAndDescFromAltDefs(ref, "<".concat(modAlt.slice(0, modAlt.length - 1).join(':'), ">"));
-      } // no parent
-
-
-      return [undefined, undefined];
-    } // note: term SNV is used instead of SNP because SO definition of SNP says
+    };
+    VCFFeature.prototype._getSOAndDescFromAltDefs = function (ref, alt) {
+        if (typeof alt === 'string' && !alt.startsWith('<')) {
+            return [undefined, undefined];
+        }
+        // look for a definition with an SO type for this
+        var soTerm = VCFFeature._altTypeToSO[alt];
+        // if no SO term but ALT is in metadata, assume sequence_variant
+        if (!soTerm && this.parser.getMetadata('ALT', alt)) {
+            soTerm = 'sequence_variant';
+        }
+        if (soTerm) {
+            return [soTerm, alt];
+        }
+        // try to look for a definition for a parent term if we can
+        var modAlt = alt.split(':');
+        if (modAlt.length > 1) {
+            return this._getSOAndDescFromAltDefs(ref, "<".concat(modAlt.slice(0, modAlt.length - 1).join(':'), ">"));
+        }
+        // no parent
+        return [undefined, undefined];
+    };
+    // note: term SNV is used instead of SNP because SO definition of SNP says
     // abundance must be at least 1% in population, and can't be sure we meet
     // that
-
-  }, {
-    key: "_getSOAndDescByExamination",
-    value: function _getSOAndDescByExamination(ref, alt) {
-      var bnd = (0, _vcf.parseBreakend)(alt);
-
-      if (bnd) {
-        return ['breakend', alt];
-      } else if (ref.length === 1 && alt.length === 1) {
-        return ['SNV', this._makeDescriptionString('SNV', ref, alt)];
-      } else if (alt === '<INS>') {
-        return ['insertion', alt];
-      } else if (alt === '<DEL>') {
-        return ['deletion', alt];
-      } else if (alt === '<INV>') {
-        return ['deletion', alt];
-      } else if (alt === '<TRA>') {
-        return ['translocation', alt];
-      } else if (alt.includes('<')) {
-        return ['sv', alt];
-      } else if (ref.length === alt.length) {
-        if (ref.split('').reverse().join('') === alt) {
-          return ['inversion', this._makeDescriptionString('inversion', ref, alt)];
+    VCFFeature.prototype._getSOAndDescByExamination = function (ref, alt) {
+        var bnd = (0, vcf_1.parseBreakend)(alt);
+        if (bnd) {
+            return ['breakend', alt];
         }
-
-        return ['substitution', this._makeDescriptionString('substitution', ref, alt)];
-      } else if (ref.length <= alt.length) {
-        return ['insertion', this._makeDescriptionString('insertion', ref, alt)];
-      } else if (ref.length > alt.length) {
-        return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
-      }
-
-      return ['indel', this._makeDescriptionString('indel', ref, alt)];
-    }
-  }, {
-    key: "_makeDescriptionString",
-    value: function _makeDescriptionString(soTerm, ref, alt) {
-      return "".concat(soTerm, " ").concat(ref, " -> ").concat(alt);
-    } // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      return _objectSpread(_objectSpread(_objectSpread({
-        uniqueId: this._id
-      }, this.variant), this.data), {}, {
-        samples: this.variant.SAMPLES
-      });
-    }
-  }]);
-  return VCFFeature;
-}();
-
+        else if (ref.length === 1 && alt.length === 1) {
+            return ['SNV', this._makeDescriptionString('SNV', ref, alt)];
+        }
+        else if (alt === '<INS>') {
+            return ['insertion', alt];
+        }
+        else if (alt === '<DEL>') {
+            return ['deletion', alt];
+        }
+        else if (alt === '<INV>') {
+            return ['deletion', alt];
+        }
+        else if (alt === '<TRA>') {
+            return ['translocation', alt];
+        }
+        else if (alt.includes('<')) {
+            return ['sv', alt];
+        }
+        else if (ref.length === alt.length) {
+            if (ref.split('').reverse().join('') === alt) {
+                return ['inversion', this._makeDescriptionString('inversion', ref, alt)];
+            }
+            return [
+                'substitution',
+                this._makeDescriptionString('substitution', ref, alt),
+            ];
+        }
+        else if (ref.length <= alt.length) {
+            return ['insertion', this._makeDescriptionString('insertion', ref, alt)];
+        }
+        else if (ref.length > alt.length) {
+            return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
+        }
+        return ['indel', this._makeDescriptionString('indel', ref, alt)];
+    };
+    VCFFeature.prototype._makeDescriptionString = function (soTerm, ref, alt) {
+        return "".concat(soTerm, " ").concat(ref, " -> ").concat(alt);
+    };
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    VCFFeature.prototype.toJSON = function () {
+        return __assign(__assign(__assign({ uniqueId: this._id }, this.variant), this.data), { samples: this.variant.SAMPLES });
+    };
+    VCFFeature._altTypeToSO = {
+        DEL: 'deletion',
+        INS: 'insertion',
+        DUP: 'duplication',
+        INV: 'inversion',
+        INVDUP: 'inverted duplication',
+        CNV: 'copy_number_variation',
+        TRA: 'translocation',
+        'DUP:TANDEM': 'tandem_duplication',
+        NON_REF: 'sequence_variant',
+        '*': 'sequence_variant',
+    };
+    return VCFFeature;
+}());
 exports.default = VCFFeature;
-(0, _defineProperty2.default)(VCFFeature, "_altTypeToSO", {
-  DEL: 'deletion',
-  INS: 'insertion',
-  DUP: 'duplication',
-  INV: 'inversion',
-  INVDUP: 'inverted duplication',
-  CNV: 'copy_number_variation',
-  TRA: 'translocation',
-  'DUP:TANDEM': 'tandem_duplication',
-  NON_REF: 'sequence_variant',
-  '*': 'sequence_variant'
-});
+//# sourceMappingURL=VcfFeature.js.map

package/dist/VcfTabixAdapter/VcfFeature.js.map

@@ -0,0 +1 @@
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