@jbrowse/plugin-variants 1.7.11 → 2.1.0

package/dist/VcfTabixAdapter/VcfTabixAdapter.test.js

@@ -1,99 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _VcfTabixAdapter = _interopRequireDefault(require("./VcfTabixAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch variants from volvox.vcf.gz', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, csiAdapter, csiFeatures, names, csiNames, features, featuresArray, csiFeaturesArray, featuresNonExist, featuresArrayNonExist;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _VcfTabixAdapter.default(_configSchema.default.create({
-            vcfGzLocation: {
-              localPath: require.resolve('./test_data/volvox.filtered.vcf.gz'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              indexType: 'TBI',
-              location: {
-                localPath: require.resolve('./test_data/volvox.filtered.vcf.gz.tbi'),
-                locationType: 'LocalPathLocation'
-              }
-            }
-          }));
-          csiAdapter = new _VcfTabixAdapter.default(_configSchema.default.create({
-            vcfGzLocation: {
-              localPath: require.resolve('./test_data/volvox.filtered.vcf.gz'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              indexType: 'CSI',
-              location: {
-                localPath: require.resolve('./test_data/volvox.filtered.vcf.gz.csi'),
-                locationType: 'LocalPathLocation'
-              }
-            }
-          }));
-          csiFeatures = csiAdapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 5;
-          return adapter.getRefNames();
-
-        case 5:
-          names = _context.sent;
-          _context.next = 8;
-          return csiAdapter.getRefNames();
-
-        case 8:
-          csiNames = _context.sent;
-          expect(names).toEqual(csiNames);
-          expect(names).toMatchSnapshot();
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context.sent;
-          _context.next = 17;
-          return csiFeatures.pipe((0, _operators.toArray)()).toPromise();
-
-        case 17:
-          csiFeaturesArray = _context.sent;
-          expect(featuresArray.slice(0, 5)).toMatchSnapshot();
-          expect(csiFeaturesArray.slice(0, 5)).toEqual(featuresArray.slice(0, 5));
-          featuresNonExist = adapter.getFeatures({
-            refName: 'ctgC',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 23;
-          return featuresNonExist.pipe((0, _operators.toArray)()).toPromise();
-
-        case 23:
-          featuresArrayNonExist = _context.sent;
-          expect(featuresArrayNonExist).toEqual([]);
-
-        case 25:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/index.test.js

@@ -1,37 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _pluginAlignments = _interopRequireDefault(require("@jbrowse/plugin-alignments"));
-
-var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = _interopRequireDefault(require("."));
-
-test('plugin in a stock JBrowse', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default(), new _pluginAlignments.default(), new _pluginSvg.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var VcfTabixAdapter = pluginManager.getAdapterType('VcfTabixAdapter');
-  var config = VcfTabixAdapter.configSchema.create({
-    type: 'VcfTabixAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-  var VariantTrack = pluginManager.getTrackType('VariantTrack');
-  var config2 = VariantTrack.configSchema.create({
-    type: 'VariantTrack',
-    trackId: 'trackId0',
-    adapter: {
-      type: 'VcfTabixAdapter'
-    }
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config2)).toMatchSnapshot();
-});