@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -0,0 +1,606 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = exports.capabilities = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _operators = require("rxjs/operators");
+
+var _util = require("../util");
+
+var _MismatchParser = require("../BamAdapter/MismatchParser");
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+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; } }
+
+function mismatchLen(mismatch) {
+  return !isInterbase(mismatch.type) ? mismatch.length : 1;
+}
+
+function isInterbase(type) {
+  return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function inc(bin, strand, type, field) {
+  var thisBin = bin[type][field];
+
+  if (!thisBin) {
+    thisBin = bin[type][field] = {
+      total: 0,
+      strands: {
+        '-1': 0,
+        '0': 0,
+        '1': 0
+      }
+    };
+  }
+
+  thisBin.total++;
+  thisBin.strands[strand]++;
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function dec(bin, strand, type, field) {
+  if (!bin[type][field]) {
+    bin[type][field] = {
+      total: 0,
+      strands: {
+        '-1': 0,
+        '0': 0,
+        '1': 0
+      }
+    };
+  }
+
+  bin[type][field].total--;
+  bin[type][field].strands[strand]--;
+}
+
+var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(SNPCoverageAdapter, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(SNPCoverageAdapter);
+
+  function SNPCoverageAdapter() {
+    (0, _classCallCheck2["default"])(this, SNPCoverageAdapter);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(SNPCoverageAdapter, [{
+    key: "configure",
+    value: function () {
+      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var _this$getSubAdapter, _this$getSubAdapter2;
+
+        var subadapterConfig, sequenceConf, dataAdapter, sequenceAdapter;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                subadapterConfig = this.getConf('subadapter');
+                sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
+                _context.next = 4;
+                return (_this$getSubAdapter = this.getSubAdapter) === null || _this$getSubAdapter === void 0 ? void 0 : _this$getSubAdapter.call(this, subadapterConfig);
+
+              case 4:
+                dataAdapter = _context.sent;
+
+                if (!sequenceConf) {
+                  _context.next = 11;
+                  break;
+                }
+
+                _context.next = 8;
+                return (_this$getSubAdapter2 = this.getSubAdapter) === null || _this$getSubAdapter2 === void 0 ? void 0 : _this$getSubAdapter2.call(this, sequenceConf);
+
+              case 8:
+                _context.t0 = _context.sent;
+                _context.next = 12;
+                break;
+
+              case 11:
+                _context.t0 = undefined;
+
+              case 12:
+                sequenceAdapter = _context.t0;
+
+                if (dataAdapter) {
+                  _context.next = 15;
+                  break;
+                }
+
+                throw new Error('Failed to get subadapter');
+
+              case 15:
+                return _context.abrupt("return", {
+                  subadapter: dataAdapter.dataAdapter,
+                  sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter
+                });
+
+              case 16:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function configure() {
+        return _configure.apply(this, arguments);
+      }
+
+      return configure;
+    }()
+  }, {
+    key: "fetchSequence",
+    value: function () {
+      var _fetchSequence2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(region) {
+        var _yield$this$configure, sequenceAdapter;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.configure();
+
+              case 2:
+                _yield$this$configure = _context2.sent;
+                sequenceAdapter = _yield$this$configure.sequenceAdapter;
+
+                if (sequenceAdapter) {
+                  _context2.next = 6;
+                  break;
+                }
+
+                return _context2.abrupt("return", undefined);
+
+              case 6:
+                return _context2.abrupt("return", (0, _util.fetchSequence)(region, sequenceAdapter));
+
+              case 7:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function fetchSequence(_x) {
+        return _fetchSequence2.apply(this, arguments);
+      }
+
+      return fetchSequence;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(region) {
+      var _this = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(observer) {
+          var _yield$_this$configur, subadapter, feats, _yield$_this$generate, bins, skipmap;
+
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  _context3.next = 2;
+                  return _this.configure();
+
+                case 2:
+                  _yield$_this$configur = _context3.sent;
+                  subadapter = _yield$_this$configur.subadapter;
+                  _context3.next = 6;
+                  return subadapter.getFeatures(region, opts).pipe((0, _operators.toArray)()).toPromise();
+
+                case 6:
+                  feats = _context3.sent;
+                  _context3.next = 9;
+                  return _this.generateCoverageBins(feats, region, opts);
+
+                case 9:
+                  _yield$_this$generate = _context3.sent;
+                  bins = _yield$_this$generate.bins;
+                  skipmap = _yield$_this$generate.skipmap;
+                  bins.forEach(function (bin, index) {
+                    observer.next(new _simpleFeature["default"]({
+                      id: "".concat(_this.id, "-").concat(region.start + index),
+                      data: {
+                        score: bin.total,
+                        snpinfo: bin,
+                        start: region.start + index,
+                        end: region.start + index + 1,
+                        refName: region.refName
+                      }
+                    }));
+                  }); // make fake features from the coverage
+
+                  Object.entries(skipmap).forEach(function (_ref2) {
+                    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+                        key = _ref3[0],
+                        skip = _ref3[1];
+
+                    observer.next(new _simpleFeature["default"]({
+                      id: key,
+                      data: {
+                        type: 'skip',
+                        start: skip.start,
+                        end: skip.end,
+                        strand: skip.strand,
+                        score: skip.score,
+                        xs: skip.xs
+                      }
+                    }));
+                  });
+                  observer.complete();
+
+                case 15:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x2) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "estimateRegionsStats",
+    value: function () {
+      var _estimateRegionsStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(regions, opts) {
+        var _yield$this$configure2, subadapter;
+
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _context4.next = 2;
+                return this.configure();
+
+              case 2:
+                _yield$this$configure2 = _context4.sent;
+                subadapter = _yield$this$configure2.subadapter;
+                return _context4.abrupt("return", subadapter.estimateRegionsStats(regions, opts));
+
+              case 5:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function estimateRegionsStats(_x3, _x4) {
+        return _estimateRegionsStats.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
+        var opts,
+            _yield$this$configure3,
+            subadapter,
+            _args5 = arguments;
+
+        return _regenerator["default"].wrap(function _callee5$(_context5) {
+          while (1) {
+            switch (_context5.prev = _context5.next) {
+              case 0:
+                opts = _args5.length > 0 && _args5[0] !== undefined ? _args5[0] : {};
+                _context5.next = 3;
+                return this.configure();
+
+              case 3:
+                _yield$this$configure3 = _context5.sent;
+                subadapter = _yield$this$configure3.subadapter;
+                return _context5.abrupt("return", subadapter.getRefNames(opts));
+
+              case 6:
+              case "end":
+                return _context5.stop();
+            }
+          }
+        }, _callee5, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }, {
+    key: "generateCoverageBins",
+    value: function () {
+      var _generateCoverageBins = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(features, region, opts) {
+        var _opts$colorBy;
+
+        var colorBy, binMax, skipmap, regionSeq, bins, _loop, i;
+
+        return _regenerator["default"].wrap(function _callee6$(_context6) {
+          while (1) {
+            switch (_context6.prev = _context6.next) {
+              case 0:
+                colorBy = opts.colorBy;
+                binMax = Math.ceil(region.end - region.start);
+                skipmap = {}; // bins contain:
+                // - cov feature if they contribute to coverage
+                // - noncov are insertions/clip features that don't contribute to coverage
+                // - delskips deletions or introns that don't contribute to coverage
+
+                if (!(features.length && (0, _util.shouldFetchReferenceSequence)((_opts$colorBy = opts.colorBy) === null || _opts$colorBy === void 0 ? void 0 : _opts$colorBy.type))) {
+                  _context6.next = 9;
+                  break;
+                }
+
+                _context6.next = 6;
+                return this.fetchSequence(region);
+
+              case 6:
+                _context6.t0 = _context6.sent;
+                _context6.next = 10;
+                break;
+
+              case 9:
+                _context6.t0 = undefined;
+
+              case 10:
+                regionSeq = _context6.t0;
+                bins = [];
+
+                _loop = function _loop(i) {
+                  var feature = features[i];
+                  var ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
+                  var fstart = feature.get('start');
+                  var fend = feature.get('end');
+                  var fstrand = feature.get('strand');
+
+                  for (var j = fstart; j < fend; j++) {
+                    var _i = j - region.start;
+
+                    if (_i >= 0 && _i < binMax) {
+                      var bin = bins[_i] || {
+                        total: 0,
+                        lowqual: {},
+                        cov: {},
+                        delskips: {},
+                        noncov: {},
+                        ref: {}
+                      };
+
+                      if (j !== fend) {
+                        bin.total++;
+                        inc(bin, fstrand, 'ref', 'ref');
+                      }
+
+                      bins[_i] = bin;
+                    }
+                  }
+
+                  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    var seq = feature.get('seq');
+                    var mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
+                    (0, _MismatchParser.getModificationPositions)(mm, seq, fstrand).forEach(function (_ref4) {
+                      var type = _ref4.type,
+                          positions = _ref4.positions;
+                      var mod = "mod_".concat(type);
+
+                      var _iterator = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(ops, positions)),
+                          _step;
+
+                      try {
+                        for (_iterator.s(); !(_step = _iterator.n()).done;) {
+                          var pos = _step.value;
+                          var epos = pos + fstart - region.start;
+
+                          if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                            var _bin = bins[epos];
+                            inc(_bin, fstrand, 'cov', mod);
+                          }
+                        }
+                      } catch (err) {
+                        _iterator.e(err);
+                      } finally {
+                        _iterator.f();
+                      }
+                    });
+                  } // methylation based coloring takes into account both reference
+                  // sequence CpG detection and reads
+                  else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+                    if (!regionSeq) {
+                      throw new Error('no region sequence detected, need sequenceAdapter configuration');
+                    }
+
+                    var _seq = feature.get('seq');
+
+                    var _mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
+
+                    var methBins = new Array(region.end - region.start).fill(0);
+                    (0, _MismatchParser.getModificationPositions)(_mm, _seq, fstrand).forEach(function (_ref5) {
+                      var type = _ref5.type,
+                          positions = _ref5.positions;
+
+                      // we are processing methylation
+                      if (type === 'm') {
+                        var _iterator2 = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(ops, positions)),
+                            _step2;
+
+                        try {
+                          for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+                            var pos = _step2.value;
+                            var epos = pos + fstart - region.start;
+
+                            if (epos >= 0 && epos < methBins.length) {
+                              methBins[epos] = 1;
+                            }
+                          }
+                        } catch (err) {
+                          _iterator2.e(err);
+                        } finally {
+                          _iterator2.f();
+                        }
+                      }
+                    });
+
+                    for (var _j = fstart; _j < fend; _j++) {
+                      var _i2 = _j - region.start;
+
+                      if (_i2 >= 0 && _i2 < bins.length - 1) {
+                        var l1 = regionSeq[_i2].toLowerCase();
+
+                        var l2 = regionSeq[_i2 + 1].toLowerCase();
+
+                        var _bin2 = bins[_i2];
+                        var bin1 = bins[_i2 + 1]; // color
+
+                        if (l1 === 'c' && l2 === 'g') {
+                          if (methBins[_i2] || methBins[_i2 + 1]) {
+                            inc(_bin2, fstrand, 'cov', 'meth');
+                            inc(bin1, fstrand, 'cov', 'meth');
+                            dec(_bin2, fstrand, 'ref', 'ref');
+                            dec(bin1, fstrand, 'ref', 'ref');
+                          } else {
+                            inc(_bin2, fstrand, 'cov', 'unmeth');
+                            inc(bin1, fstrand, 'cov', 'unmeth');
+                            dec(_bin2, fstrand, 'ref', 'ref');
+                            dec(bin1, fstrand, 'ref', 'ref');
+                          }
+                        }
+                      }
+                    }
+                  } // normal SNP based coloring
+                  else {
+                    var mismatches = feature.get('mismatches');
+
+                    if (mismatches) {
+                      for (var _i3 = 0; _i3 < mismatches.length; _i3++) {
+                        var mismatch = mismatches[_i3];
+                        var mstart = fstart + mismatch.start;
+
+                        for (var _j2 = mstart; _j2 < mstart + mismatchLen(mismatch); _j2++) {
+                          var epos = _j2 - region.start;
+
+                          if (epos >= 0 && epos < bins.length) {
+                            var _bin3 = bins[epos];
+                            var base = mismatch.base,
+                                type = mismatch.type;
+                            var interbase = isInterbase(type);
+
+                            if (!interbase) {
+                              dec(_bin3, fstrand, 'ref', 'ref');
+                            } else {
+                              inc(_bin3, fstrand, 'noncov', type);
+                            }
+
+                            if (type === 'deletion' || type === 'skip') {
+                              inc(_bin3, fstrand, 'delskips', type);
+                              _bin3.total--;
+                            } else if (!interbase) {
+                              inc(_bin3, fstrand, 'cov', base);
+                            }
+                          }
+                        }
+                      }
+
+                      mismatches.filter(function (mismatch) {
+                        return mismatch.type === 'skip';
+                      }).forEach(function (mismatch) {
+                        var mstart = feature.get('start') + mismatch.start;
+                        var start = mstart;
+                        var end = mstart + mismatch.length;
+                        var strand = feature.get('strand');
+                        var hash = "".concat(start, "_").concat(end, "_").concat(strand);
+
+                        if (!skipmap[hash]) {
+                          skipmap[hash] = {
+                            feature: feature,
+                            start: start,
+                            end: end,
+                            strand: strand,
+                            xs: (0, _util.getTag)(feature, 'XS') || (0, _util.getTag)(feature, 'TS'),
+                            score: 1
+                          };
+                        } else {
+                          skipmap[hash].score++;
+                        }
+                      });
+                    }
+                  }
+                };
+
+                for (i = 0; i < features.length; i++) {
+                  _loop(i);
+                }
+
+                return _context6.abrupt("return", {
+                  bins: bins,
+                  skipmap: skipmap
+                });
+
+              case 15:
+              case "end":
+                return _context6.stop();
+            }
+          }
+        }, _callee6, this);
+      }));
+
+      function generateCoverageBins(_x5, _x6, _x7) {
+        return _generateCoverageBins.apply(this, arguments);
+      }
+
+      return generateCoverageBins;
+    }()
+  }]);
+  return SNPCoverageAdapter;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = SNPCoverageAdapter;
+var capabilities = SNPCoverageAdapter.capabilities;
+exports.capabilities = capabilities;

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/SNPCoverageAdapter/configSchema.js

@@ -0,0 +1,22 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _default = function _default(pluginManager) {
+  return _mobxStateTree.types.late(function () {
+    return (0, _configuration.ConfigurationSchema)('SNPCoverageAdapter', {
+      subadapter: pluginManager.pluggableConfigSchemaType('adapter')
+    }, {
+      explicitlyTyped: true
+    });
+  });
+};
+
+exports["default"] = _default;

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/SNPCoverageAdapter/index.js

@@ -0,0 +1,45 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _SNPCoverageAdapter = require("./SNPCoverageAdapter");
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var _default = function _default(pluginManager) {
+  pluginManager.addAdapterType(function () {
+    return new _AdapterType["default"]({
+      name: 'SNPCoverageAdapter',
+      adapterMetadata: {
+        category: null,
+        displayName: null,
+        hiddenFromGUI: true,
+        description: null
+      },
+      getAdapterClass: function getAdapterClass() {
+        return Promise.resolve().then(function () {
+          return _interopRequireWildcard(require('./SNPCoverageAdapter'));
+        }).then(function (r) {
+          return r["default"];
+        });
+      },
+      configSchema: (0, _configSchema["default"])(pluginManager),
+      adapterCapabilities: _SNPCoverageAdapter.capabilities
+    });
+  });
+};
+
+exports["default"] = _default;