@jbrowse/plugin-alignments 1.7.11 → 2.1.0

package/dist/BamAdapter/MismatchParser.test.js

@@ -1,251 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _MismatchParser = require("./MismatchParser");
-
-var seq = 'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTT'; // examples come from https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-// and http://seqanswers.com/forums/showthread.php?t=8978
-
-test('cigar to mismatches', function () {
-  expect((0, _MismatchParser.cigarToMismatches)((0, _MismatchParser.parseCigar)('56M1D45M'), seq)).toEqual([{
-    start: 56,
-    type: 'deletion',
-    base: '*',
-    length: 1
-  }]);
-});
-test('md to mismatches', function () {
-  var cigarMismatches = (0, _MismatchParser.cigarToMismatches)((0, _MismatchParser.parseCigar)('56M1D45M'), seq);
-  expect((0, _MismatchParser.mdToMismatches)('10A80', (0, _MismatchParser.parseCigar)('56M1D45M'), cigarMismatches, seq)).toEqual([{
-    start: 10,
-    type: 'mismatch',
-    base: 'C',
-    altbase: 'A',
-    length: 1
-  }]);
-});
-describe('get mismatches', function () {
-  it('simple deletion', function () {
-    // simple deletion
-    expect((0, _MismatchParser.getMismatches)('56M1D45M', '56^A45', seq)).toEqual([{
-      start: 56,
-      type: 'deletion',
-      base: '*',
-      length: 1
-    }]);
-  });
-  it('simple insertion', function () {
-    // simple insertion
-    expect((0, _MismatchParser.getMismatches)('89M1I11M', '100', 'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTA')).toEqual([{
-      start: 89,
-      type: 'insertion',
-      base: '1',
-      length: 0
-    }]);
-  });
-  it('deletion and a SNP', function () {
-    // contains a deletion and a SNP
-    // read GGGGG--ATTTTTT
-    //      |||||   ||||||
-    //      GGGGGACCTTTTTT
-    expect((0, _MismatchParser.getMismatches)('5M2D6M', '5^AC0C5', 'GGGGGATTTTTT')).toEqual([{
-      start: 5,
-      type: 'deletion',
-      base: '*',
-      length: 2
-    }, {
-      start: 7,
-      type: 'mismatch',
-      base: 'A',
-      altbase: 'C',
-      length: 1
-    }]);
-  });
-  it('0-length MD entries', function () {
-    // 0-length MD entries, which indicates two SNPs right next to each other
-    // "They generally occur between SNPs, or between a deletion then a SNP."
-    // http://seqanswers.com/forums/showthread.php?t=8978
-    //
-    // read GGGGGCATTTTT
-    //      |||||  |||||
-    // ref  GGGGGACTTTTT
-    expect((0, _MismatchParser.getMismatches)('12M', '5A0C5', 'GGGGGCATTTTT')).toEqual([{
-      altbase: 'A',
-      base: 'C',
-      length: 1,
-      start: 5,
-      type: 'mismatch'
-    }, {
-      altbase: 'C',
-      base: 'A',
-      length: 1,
-      start: 6,
-      type: 'mismatch'
-    }]);
-  });
-  it('non-0-length-MD string', function () {
-    // same as above but with the non-0-length MD string
-    // not sure if it is entirely legal, but may appear in the wild
-    expect((0, _MismatchParser.getMismatches)('12M', '5AC5', 'GGGGGCATTTTT')).toEqual([{
-      altbase: 'A',
-      base: 'C',
-      length: 1,
-      start: 5,
-      type: 'mismatch'
-    }, {
-      altbase: 'C',
-      base: 'A',
-      length: 1,
-      start: 6,
-      type: 'mismatch'
-    }]);
-  });
-});
-test('basic skip', function () {
-  expect((0, _MismatchParser.getMismatches)('6M200N6M', '5AC5', 'GGGGGCATTTTT')).toEqual([{
-    base: 'N',
-    length: 200,
-    start: 6,
-    type: 'skip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 5,
-    type: 'mismatch'
-  }, {
-    altbase: 'C',
-    base: 'A',
-    length: 1,
-    start: 206,
-    type: 'mismatch'
-  }]);
-});
-test('vsbuffalo', function () {
-  // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 1
-  expect((0, _MismatchParser.getMismatches)('89M1I11M', '100', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')).toEqual([{
-    base: '1',
-    length: 0,
-    start: 89,
-    type: 'insertion'
-  }]); // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 2
-
-  expect((0, _MismatchParser.getMismatches)('9M1I91M', '48T42G8', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')).toEqual([{
-    base: '1',
-    length: 0,
-    start: 9,
-    type: 'insertion'
-  }, {
-    altbase: 'T',
-    base: 'A',
-    length: 1,
-    start: 48,
-    type: 'mismatch'
-  }, {
-    altbase: 'G',
-    base: 'A',
-    length: 1,
-    start: 91,
-    type: 'mismatch'
-  }]);
-});
-test('more skip', function () {
-  expect((0, _MismatchParser.getMismatches)('3M200N3M200N3M', '8A', 'GGGGGCATTTTT')).toEqual([{
-    base: 'N',
-    length: 200,
-    start: 3,
-    type: 'skip'
-  }, {
-    base: 'N',
-    length: 200,
-    start: 206,
-    type: 'skip'
-  }, {
-    altbase: 'A',
-    base: 'T',
-    length: 1,
-    start: 408,
-    type: 'mismatch'
-  }]);
-  expect((0, _MismatchParser.getMismatches)('31M1I17M1D37M', '6G4C20G1A5C5A1^C3A15G1G15', seq).sort(function (a, b) {
-    return a.start - b.start;
-  })).toMatchInlineSnapshot("\n    Array [\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"A\",\n        \"length\": 1,\n        \"start\": 6,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"C\",\n        \"base\": \"A\",\n        \"length\": 1,\n        \"start\": 11,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"base\": \"1\",\n        \"length\": 0,\n        \"start\": 31,\n        \"type\": \"insertion\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 32,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 34,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"C\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 40,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 46,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"base\": \"*\",\n        \"length\": 1,\n        \"start\": 48,\n        \"type\": \"deletion\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 52,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 68,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 70,\n        \"type\": \"mismatch\",\n      },\n    ]\n  ");
-});
-test('clipping', function () {
-  expect((0, _MismatchParser.getMismatches)('200H10M200H', '9A', 'AAAAAAAAAC')).toEqual([{
-    cliplen: 200,
-    base: 'H200',
-    length: 1,
-    start: 0,
-    type: 'hardclip'
-  }, {
-    cliplen: 200,
-    base: 'H200',
-    length: 1,
-    start: 10,
-    type: 'hardclip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 9,
-    type: 'mismatch'
-  }]);
-  expect((0, _MismatchParser.getMismatches)('10S10M10S', '9A', 'AAAAAAAAAAGGGGGGGGGC')).toEqual([{
-    cliplen: 10,
-    base: 'S10',
-    length: 1,
-    start: 0,
-    type: 'softclip'
-  }, {
-    cliplen: 10,
-    base: 'S10',
-    length: 1,
-    start: 10,
-    type: 'softclip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 9,
-    type: 'mismatch'
-  }]);
-});
-test('getNextRefPos test 1', function () {
-  var cigar = (0, _MismatchParser.parseCigar)('10S10M1I4M1D15M');
-  var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15, 20, 25, 30, 35]);
-  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5, 15, 20, 25]);
-});
-test('getNextRefPos test 2', function () {
-  var cigar = (0, _MismatchParser.parseCigar)('10S15M');
-  var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15]);
-  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5]);
-});
-test('getModificationPositions', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-}); // ? means "modification status of the skipped bases provided."
-
-test('getModificationPositions with unknown (?)', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m?,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-}); // . means "modification status of the skipped bases is low probability"
-
-test('getModificationPositions with unknown (.)', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m.,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-});

package/dist/CramAdapter/CramAdapter.test.js

@@ -1,138 +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 _genericFilehandle = require("generic-filehandle");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _CramAdapter = _interopRequireDefault(require("./CramAdapter"));
-
-var _CramTestAdapters = require("./CramTestAdapters");
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var pluginManager = new _PluginManager.default();
-var configSchema = pluginManager.load(_configSchema.default);
-
-var getVolvoxSequenceSubAdapter = /*#__PURE__*/function () {
-  var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            return _context.abrupt("return", {
-              dataAdapter: new _CramTestAdapters.SequenceAdapter(new _genericFilehandle.LocalFile(require.resolve('../../test_data/volvox.fa'))),
-              sessionIds: new Set()
-            });
-
-          case 1:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-
-  return function getVolvoxSequenceSubAdapter() {
-    return _ref.apply(this, arguments);
-  };
-}();
-
-test('adapter can fetch features from volvox-sorted.cram', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _CramAdapter.default(configSchema.create({
-            cramLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-              locationType: 'LocalPathLocation'
-            },
-            craiLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-              locationType: 'LocalPathLocation'
-            }
-          }), getVolvoxSequenceSubAdapter, pluginManager);
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context2.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context2.sent;
-          expect(featuresArray[0].get('refName')).toBe('ctgA');
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.length).toEqual(3809);
-          expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
-          expect(adapter.refIdToName(0)).toBe('ctgA');
-          expect(adapter.refIdToName(1)).toBe(undefined);
-          _context2.t0 = expect;
-          _context2.next = 14;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 14:
-          _context2.t1 = _context2.sent;
-          (0, _context2.t0)(_context2.t1).toBe(true);
-
-        case 16:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var adapter, features, featuresArray, f;
-  return _regenerator.default.wrap(function _callee3$(_context3) {
-    while (1) {
-      switch (_context3.prev = _context3.next) {
-        case 0:
-          adapter = new _CramAdapter.default(configSchema.create({
-            cramLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-              locationType: 'LocalPathLocation'
-            },
-            craiLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-              locationType: 'LocalPathLocation'
-            }
-          }), getVolvoxSequenceSubAdapter, pluginManager);
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 100
-          });
-          _context3.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context3.sent;
-          f = featuresArray[0].toJSON();
-          expect(f.refName).toBe('ctgA');
-          expect(f.start).toBe(2);
-          expect(f.end).toBe(102); // don't pass the mismatches to the frontend
-
-          expect(f.mismatches).toEqual(undefined);
-
-        case 10:
-        case "end":
-          return _context3.stop();
-      }
-    }
-  }, _callee3);
-})));

package/dist/LinearAlignmentsDisplay/models/configSchema.test.js

@@ -1,83 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-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 _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
-
-var _pluginSvg = require("@jbrowse/plugin-svg");
-
-var _PileupRenderer = _interopRequireDefault(require("../../PileupRenderer"));
-
-var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRenderer"));
-
-var _LinearPileupDisplay = _interopRequireDefault(require("../../LinearPileupDisplay"));
-
-var _LinearSNPCoverageDisplay = _interopRequireDefault(require("../../LinearSNPCoverageDisplay"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-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; } }
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(function () {
-  jest.spyOn(console, 'warn').mockImplementation(function () {});
-});
-afterEach(function () {
-  console.warn.mockRestore();
-});
-
-var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(AlignmentsPlugin, _Plugin);
-
-  var _super = _createSuper(AlignmentsPlugin);
-
-  function AlignmentsPlugin() {
-    (0, _classCallCheck2.default)(this, AlignmentsPlugin);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(AlignmentsPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      (0, _PileupRenderer.default)(pluginManager);
-      pluginManager.addRendererType(function () {
-        return new _BoxRendererType.default({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
-          configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
-          pluginManager: pluginManager
-        });
-      });
-      (0, _SNPCoverageRenderer.default)(pluginManager);
-      (0, _LinearPileupDisplay.default)(pluginManager);
-      (0, _LinearSNPCoverageDisplay.default)(pluginManager);
-    }
-  }]);
-  return AlignmentsPlugin;
-}(_Plugin2.default);
-
-test('has a type attr', function () {
-  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new AlignmentsPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearAlignmentsDisplay',
-    displayId: 'display0',
-    name: 'Zonker Display'
-  });
-  expect(config.type).toEqual('LinearAlignmentsDisplay');
-});

package/dist/LinearPileupDisplay/configSchema.test.js

@@ -1,92 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-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 _Plugin3 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
-
-var _pluginSvg = require("@jbrowse/plugin-svg");
-
-var _PileupRenderer = _interopRequireDefault(require("../PileupRenderer"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-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; } }
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(function () {
-  jest.spyOn(console, 'warn').mockImplementation(function () {});
-});
-afterEach(function () {
-  console.warn.mockRestore();
-});
-
-var PileupRendererPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(PileupRendererPlugin, _Plugin);
-
-  var _super = _createSuper(PileupRendererPlugin);
-
-  function PileupRendererPlugin() {
-    (0, _classCallCheck2.default)(this, PileupRendererPlugin);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(PileupRendererPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      (0, _PileupRenderer.default)(pluginManager);
-    }
-  }]);
-  return PileupRendererPlugin;
-}(_Plugin3.default);
-
-var SvgFeatureRendererPlugin = /*#__PURE__*/function (_Plugin2) {
-  (0, _inherits2.default)(SvgFeatureRendererPlugin, _Plugin2);
-
-  var _super2 = _createSuper(SvgFeatureRendererPlugin);
-
-  function SvgFeatureRendererPlugin() {
-    (0, _classCallCheck2.default)(this, SvgFeatureRendererPlugin);
-    return _super2.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(SvgFeatureRendererPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addRendererType(function () {
-        return new _BoxRendererType.default({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
-          configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
-          pluginManager: pluginManager
-        });
-      });
-    }
-  }]);
-  return SvgFeatureRendererPlugin;
-}(_Plugin3.default);
-
-test('has a type attr', function () {
-  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearPileupDisplay',
-    displayId: 'display0',
-    name: 'Zonker Display'
-  });
-  expect(config.type).toEqual('LinearPileupDisplay');
-});

package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js

@@ -1,62 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-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 _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRenderer"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-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; } }
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(function () {
-  jest.spyOn(console, 'warn').mockImplementation(function () {});
-});
-afterEach(function () {
-  console.warn.mockRestore();
-}); // change renderer
-
-var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
-
-  var _super = _createSuper(SNPCoverageRendererPlugin);
-
-  function SNPCoverageRendererPlugin() {
-    (0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(SNPCoverageRendererPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      (0, _SNPCoverageRenderer.default)(pluginManager);
-    }
-  }]);
-  return SNPCoverageRendererPlugin;
-}(_Plugin2.default);
-
-test('has a type attr', function () {
-  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearSNPCoverageDisplay',
-    displayId: 'display1',
-    name: 'SNPZonker Display'
-  });
-  expect(config.type).toEqual('LinearSNPCoverageDisplay');
-});

package/dist/PileupRenderer/components/PileupRendering.test.js

@@ -1,36 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PrecomputedLayout = _interopRequireDefault(require("@jbrowse/core/util/layouts/PrecomputedLayout"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _PileupRendering = _interopRequireDefault(require("./PileupRendering"));
-
-// these tests do very little, let's try to expand them at some point
-test('one', function () {
-  var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_PileupRendering.default, {
-    width: 500,
-    height: 500,
-    regions: [{
-      refName: 'zonk',
-      start: 1,
-      end: 3
-    }],
-    layout: new _PrecomputedLayout.default({
-      rectangles: {},
-      totalHeight: 20
-    }),
-    displayModel: {},
-    bpPerPx: 3,
-    config: {
-      type: 'DummyRenderer'
-    }
-  })),
-      container = _render.container;
-
-  expect(container.firstChild).toMatchSnapshot();
-});

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";