@jbrowse/core 1.7.11 → 2.1.0

package/util/index.test.js

@@ -1,213 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _index = require("./index");
-
-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; }
-
-describe('parseLocString', function () {
-  var cases = [['chr1:1..200', {
-    start: 0,
-    end: 200,
-    refName: 'chr1'
-  }], ['chr1:1,000,000..2,000,000', {
-    start: 999999,
-    end: 2000000,
-    refName: 'chr1'
-  }], ['chr1:1-200', {
-    start: 0,
-    end: 200,
-    refName: 'chr1'
-  }], ['{hg19}chr1:1-200', {
-    assemblyName: 'hg19',
-    start: 0,
-    end: 200,
-    refName: 'chr1'
-  }], ['{hg19}chr1:1..200', {
-    assemblyName: 'hg19',
-    start: 0,
-    end: 200,
-    refName: 'chr1'
-  }], ['{hg19}chr1:1', {
-    assemblyName: 'hg19',
-    start: 0,
-    end: 1,
-    refName: 'chr1'
-  }], ['chr1:1', {
-    start: 0,
-    end: 1,
-    refName: 'chr1'
-  }], ['chr1:-1', {
-    start: -2,
-    end: -1,
-    refName: 'chr1'
-  }], ['chr1:-100..-1', {
-    start: -101,
-    end: -1,
-    refName: 'chr1'
-  }], ['chr1:-100--1', // weird but valid
-  {
-    start: -101,
-    end: -1,
-    refName: 'chr1'
-  }], ['chr2:1000-', {
-    refName: 'chr2',
-    start: 999
-  }], ['chr2:1,000-', {
-    refName: 'chr2',
-    start: 999
-  }], ['chr1', {
-    refName: 'chr1'
-  }], ['{hg19}chr1', {
-    assemblyName: 'hg19',
-    refName: 'chr1'
-  }]]; // test unreversed
-
-  cases.forEach(function (_ref) {
-    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-        input = _ref2[0],
-        output = _ref2[1];
-
-    test("".concat(input), function () {
-      expect((0, _index.parseLocString)(input, function (refName) {
-        return ['chr1', 'chr2'].includes(refName);
-      })).toEqual(_objectSpread(_objectSpread({}, output), {}, {
-        reversed: false
-      }));
-    });
-  }); // test reversed
-
-  cases.forEach(function (_ref3) {
-    var _ref4 = (0, _slicedToArray2.default)(_ref3, 2),
-        input = _ref4[0],
-        output = _ref4[1];
-
-    test("".concat(input), function () {
-      expect((0, _index.parseLocString)(input + '[rev]', function (refName) {
-        return ['chr1', 'chr2'].includes(refName);
-      })).toEqual(_objectSpread(_objectSpread({}, output), {}, {
-        reversed: true
-      }));
-    });
-  });
-});
-describe('assembleLocString', function () {
-  var cases = [[{
-    refName: 'chr1'
-  }, 'chr1'], [{
-    refName: 'chr1',
-    start: 0
-  }, 'chr1:1..'], [{
-    refName: 'chr1',
-    start: 0,
-    end: 1
-  }, 'chr1:1'], [{
-    refName: 'chr1',
-    start: 0,
-    end: 100
-  }, 'chr1:1..100'], [{
-    refName: 'chr1',
-    start: 0,
-    end: 200
-  }, 'chr1:1..200'], [{
-    refName: 'chr1',
-    start: 1000000,
-    end: 2000000
-  }, 'chr1:1,000,001..2,000,000'], [{
-    assemblyName: 'hg19',
-    refName: 'chr1',
-    start: 0,
-    end: 100
-  }, '{hg19}chr1:1..100'], [{
-    refName: 'chr1',
-    start: -2,
-    end: -1
-  }, 'chr1:-1'], [{
-    start: -100,
-    end: -1,
-    refName: 'chr1'
-  }, 'chr1:-99..-1']];
-  cases.forEach(function (_ref5) {
-    var _ref6 = (0, _slicedToArray2.default)(_ref5, 2),
-        input = _ref6[0],
-        output = _ref6[1];
-
-    test("assemble ".concat(output), function () {
-      expect((0, _index.assembleLocString)(input)).toEqual(output);
-    });
-    test("assemble and parse ".concat(output), function () {
-      expect((0, _index.parseLocString)((0, _index.assembleLocString)(input), function (refName) {
-        return refName === 'chr1' || refName === 'chr2';
-      })).toEqual(_objectSpread(_objectSpread({}, input), {}, {
-        reversed: false
-      }));
-    });
-  }); // Special case since undefined `start` will result in `start` being assumed
-  // to be `0`
-
-  var location = {
-    refName: 'chr1',
-    end: 100
-  };
-  test("assemble 'chr1:1..100'", function () {
-    expect((0, _index.assembleLocString)(location)).toEqual('chr1:1..100');
-  });
-  test('test empty assemblyName', function () {
-    var location = '{}chr1:1..100';
-    expect(function () {
-      (0, _index.parseLocString)(location, function (refName) {
-        return refName === 'chr1' || refName === 'chr2';
-      });
-    }).toThrow("no assembly name was provided in location \"".concat(location, "\""));
-  });
-  test("assemble and parse 'chr1:1..100'", function () {
-    expect((0, _index.parseLocString)((0, _index.assembleLocString)(location), function (refName) {
-      return refName === 'chr1' || refName === 'chr2';
-    })).toEqual(_objectSpread(_objectSpread({}, location), {}, {
-      start: 0,
-      reversed: false,
-      assemblyName: undefined
-    }));
-  });
-});
-describe('compareLocStrings', function () {
-  var cases = [['chr1:1..200', 'chr1:1-200', 0], ['chr1:1-200', '{hg19}chr1:1-200', -1], ['{hg19}chr1:1-200', 'chr1:1-200', 1], ['{hg19}chr1:1-200', '{hg19}chr1:2-200', -1]];
-  cases.forEach(function (_ref7) {
-    var _ref8 = (0, _slicedToArray2.default)(_ref7, 3),
-        input1 = _ref8[0],
-        input2 = _ref8[1],
-        output = _ref8[2];
-
-    test("".concat(input1, " ").concat(input2, " = ").concat(output), function () {
-      expect((0, _index.compareLocStrings)(input1, input2, function (refName) {
-        return refName === 'chr1' || refName === 'chr2';
-      })).toEqual(output);
-    });
-  });
-});
-describe('test stringify', function () {
-  var testStringify = {
-    refName: 'ctgA',
-    start: 5000,
-    end: 20000,
-    reversed: false,
-    assemblyName: 'volvox',
-    oob: false,
-    offset: 0,
-    coord: 5001,
-    index: 0
-  };
-  test('stringify refName: bp', function () {
-    expect((0, _index.stringify)({
-      coord: testStringify.offset,
-      refName: testStringify.refName
-    })).toBe('ctgA:0');
-  });
-});

package/util/jexlStrings.test.js

@@ -1,48 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _jexlStrings = require("./jexlStrings");
-
-var _simpleFeature = _interopRequireDefault(require("./simpleFeature"));
-
-/* eslint-disable no-underscore-dangle */
-describe('function string parsing', function () {
-  it('can detect a jexl expression', function () {
-    var str = 'jexl:a+b+c+5';
-    expect(str.startsWith('jexl:')).toBeTruthy();
-  });
-  it('can create a jexl expression', function () {
-    var str = 'jexl:a+b+c+5';
-    var expr = (0, _jexlStrings.stringToJexlExpression)(str);
-    expect(expr._exprStr).toEqual('a+b+c+5');
-  });
-  it('can create a jexl expression 2', function () {
-    var str = 'jexl:\na+b+c+5';
-    var expr = (0, _jexlStrings.stringToJexlExpression)(str);
-    expect(expr._exprStr).toEqual('\na+b+c+5');
-    var result = expr.evalSync({
-      a: 5,
-      b: 10,
-      c: 15
-    });
-    expect(result).toEqual(35);
-  });
-  it('can use the loaded core helper functions to access feature info', function () {
-    var feature = new _simpleFeature.default({
-      uniqueId: 'jexlFeature',
-      score: 10,
-      start: 1,
-      end: 9
-    });
-    expect((0, _jexlStrings.stringToJexlExpression)("jexl:get(feature,'score')").evalSync({
-      feature: feature
-    })).toEqual(10);
-    expect((0, _jexlStrings.stringToJexlExpression)("jexl:get(feature,'uniqueId')").evalSync({
-      feature: feature
-    })).toBe('jexlFeature');
-    expect((0, _jexlStrings.stringToJexlExpression)("jexl:get(feature,'end') - get(feature,'start') == 8").evalSync({
-      feature: feature
-    })).toBe(true);
-  });
-});

package/util/layouts/GranularRectLayout.test.js

@@ -1,99 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _GranularRectLayout = _interopRequireDefault(require("./GranularRectLayout"));
-
-describe('GranularRectLayout', function () {
-  it('lays out non-overlapping features end to end', function () {
-    var l = new _GranularRectLayout.default({
-      pitchX: 10,
-      pitchY: 4
-    });
-    var testRects = [['1,0', 4133, 5923, 16], ['1,1', 11299, 12389, 16], ['1,2', 21050, 22778, 16], ['1,3', 41125, 47459, 16], ['1,4', 47926, 49272, 16], ['1,5', 50240, 52495, 16], ['1,6', 53329, 56283, 16], ['1,7', 59309, 79441, 16], ['1,8', 80359, 83196, 16], ['1,9', 92147, 94188, 16], ['1,10', 96241, 103626, 16], ['1,11', 104396, 108110, 16], ['1,12', 111878, 125251, 16], ['1,13', 125747, 128085, 16], ['1,14', 131492, 132641, 16], ['1,15', 133857, 134931, 16], ['1,16', 137023, 138220, 16], ['1,17', 140703, 145668, 16], ['1,18', 146045, 147059, 16], ['1,19', 162296, 165395, 16], ['1,20', 168531, 170795, 16], ['1,21', 174812, 180475, 16], ['1,22', 184302, 188826, 16], ['1,23', 189609, 191141, 16], ['1,24', 199799, 201389, 16], ['1,25', 203436, 211345, 16], ['1,26', 212100, 212379, 16], ['1,27', 213418, 214627, 16], ['1,28', 215115, 219344, 16], ['1,29', 220067, 222525, 16], ['1,30', 223308, 228141, 16], ['1,31', 234473, 236768, 16], ['1,32', 239691, 245015, 16]];
-
-    for (var i = 0; i < testRects.length; i += 1) {
-      var top = l.addRect.apply(l, (0, _toConsumableArray2.default)(testRects[i]));
-      expect(top).toEqual(0);
-    }
-  });
-  it('stacks up overlapping features', function () {
-    var l = new _GranularRectLayout.default({
-      pitchX: 10,
-      pitchY: 4
-    });
-    var testRects = [];
-
-    for (var i = 1; i <= 20; i += 1) {
-      testRects.push(["feature-".concat(i), 100 * i - 60, 100 * i + 60, 1]);
-    }
-
-    for (var _i = 0; _i < testRects.length; _i += 1) {
-      var top = l.addRect.apply(l, (0, _toConsumableArray2.default)(testRects[_i]));
-      expect(top).toEqual(_i % 2 * 4);
-    }
-  });
-  it('discards regions', function () {
-    var l = new _GranularRectLayout.default({
-      pitchX: 10,
-      pitchY: 4
-    });
-
-    for (var i = 0; i < 20; i += 1) {
-      var top = l.addRect("feature-".concat(i), 10000 * i + 4000, 10000 * i + 16000, 1);
-      expect(top).toEqual(i % 2 * 4);
-    }
-
-    expect(l.bitmap[0].rowState.bits.length).toBe(34812);
-    expect(l.bitmap[1].rowState.bits.length).toBe(34812);
-    l.discardRange(190000, 220000);
-    expect(l.bitmap[0].rowState.bits.length).toBe(24802);
-    expect(l.bitmap[1].rowState.bits.length).toBe(23802);
-    l.discardRange(0, 100000);
-    expect(l.bitmap[0].rowState.bits.length).toBe(19001);
-    expect(l.bitmap[1].rowState.bits.length).toBe(23802);
-    l.discardRange(0, 220000);
-    expect(l.bitmap[0].rowState).toBeUndefined();
-  }); // see issue #486
-
-  it('tests that adding +/- pitchX fixes resolution causing errors', function () {
-    var l = new _GranularRectLayout.default({
-      pitchX: 91.21851599727707,
-      pitchY: 3
-    });
-    l.addRect('test', 2581541, 2581542, 1);
-    expect(l.serializeRegion({
-      start: 2581491,
-      end: 2818659
-    }).rectangles.test).toBeTruthy();
-  });
-  it('tests reinitializing layout due to throwing away old one', function () {
-    var spy = jest.spyOn(console, 'warn').mockImplementation(function () {});
-    var l = new _GranularRectLayout.default({
-      pitchX: 1,
-      pitchY: 1,
-      maxHeight: 600
-    });
-    l.addRect('test1', 0, 10000, 1);
-    l.addRect('test2', 1000000, 1000100, 1);
-    l.addRect('test3', 0, 10000, 1);
-    expect(l.rectangles.size).toBe(3);
-    expect(spy).toHaveBeenCalled();
-    spy.mockRestore();
-  });
-  it('tests adding a gigantic feature that fills entire row with another smaller added on top', function () {
-    var l = new _GranularRectLayout.default({
-      pitchX: 100,
-      pitchY: 1,
-      maxHeight: 600
-    });
-    expect(l.getByCoord(50000, 0)).toEqual(undefined);
-    l.addRect('test1', 0, 100000000, 1, 'feat1');
-    expect(l.getByCoord(50000, 0)).toEqual('test1');
-    l.addRect('test2', 0, 1000, 1, 'feat2');
-    expect(l.getByCoord(500, 1)).toEqual('test2');
-    expect(l.rectangles.size).toBe(2);
-  });
-});

package/util/range.test.js

@@ -1,64 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _range = require("./range");
-
-describe('insersection2', function () {
-  var testCases = [{
-    in: [1, 3, 5, 10],
-    out: []
-  }, {
-    in: [1, 1, 2, 2],
-    out: []
-  }, {
-    in: [1, 2, 1, 2],
-    out: [1, 2]
-  }, {
-    in: [1, 3, 2, 4],
-    out: [2, 3]
-  }, {
-    in: [2, 4, 1, 3],
-    out: [2, 3]
-  }, {
-    in: [2, 4, 1, 4],
-    out: [2, 4]
-  }, {
-    in: [1, 4, 2, 4],
-    out: [2, 4]
-  }, {
-    in: [1, 3, 1, 4],
-    out: [1, 3]
-  }, {
-    in: [1, 4, 1, 3],
-    out: [1, 3]
-  }, {
-    in: [2, 3, 1, 2],
-    out: []
-  }, {
-    in: [1, 2, 2, 3],
-    out: []
-  }, {
-    in: [1, 1, 1, 1],
-    out: []
-  }, {
-    in: [1, 1, 1, 2],
-    out: []
-  }, {
-    in: [1, 2, 1, 1],
-    out: []
-  }, {
-    in: [1, 3, 2, 2],
-    out: []
-  }, {
-    in: [2, 2, 1, 3],
-    out: []
-  }];
-  testCases.forEach(function (testcase) {
-    test("intersection2(".concat(testcase.in, ") -> ").concat(testcase.out), function () {
-      expect(_range.intersection2.apply(void 0, (0, _toConsumableArray2.default)(testcase.in))).toEqual(testcase.out);
-    });
-  });
-});

package/util/simpleFeature.test.js

@@ -1,34 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _simpleFeature = _interopRequireDefault(require("./simpleFeature"));
-
-test('can create a simple feature', function () {
-  var f = new _simpleFeature.default({
-    uniqueId: 'test',
-    start: 100,
-    end: 200
-  });
-  expect(f.id()).toEqual('test');
-  expect(f.get('start')).toEqual(100);
-  expect(f.get('end')).toEqual(200);
-});
-test('can create a simple with subfeatures', function () {
-  var f = new _simpleFeature.default({
-    uniqueId: 'test',
-    start: 100,
-    end: 500,
-    subfeatures: [{
-      start: 100,
-      end: 200
-    }, {
-      start: 400,
-      end: 500
-    }]
-  });
-  expect(f.id()).toEqual('test');
-  expect(f.get('start')).toEqual(100);
-  expect(f.get('end')).toEqual(500);
-  expect(f.get('subfeatures')[0].get('start')).toEqual(100);
-});

package/util/stats.test.js

@@ -1,172 +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 _simpleFeature = _interopRequireDefault(require("./simpleFeature"));
-
-var _rxjs = require("rxjs");
-
-var _stats = require("./stats");
-
-test('calc std', function () {
-  var s = [1, 2, 3];
-  var sum = s.reduce(function (a, b) {
-    return a + b;
-  });
-  var sumSq = s.reduce(function (a, b) {
-    return a + b * b;
-  });
-  expect((0, _stats.calcStdFromSums)(sum, sumSq, s.length, true)).toBeCloseTo(0.8164965809); // calculated from a webapp
-
-  expect((0, _stats.calcStdFromSums)(sum, sumSq, s.length, false)).toBeCloseTo(1); // calculated from a webapp
-
-  expect((0, _stats.calcStdFromSums)(100, 100, 0)).toEqual(0); // fake thing where list "n" is 0
-
-  expect((0, _stats.calcStdFromSums)(100000, 100, 5)).toEqual(0); // fake thing where sumSq probably wrong
-});
-test('test rectify', function () {
-  // mean of 0 bases covered = 0
-  expect((0, _stats.rectifyStats)({
-    basesCovered: 0
-  }).scoreMean).toEqual(0);
-  var s = (0, _stats.rectifyStats)({
-    featureCount: 10,
-    scoreSum: 1000
-  });
-  expect(s.scoreMean).toEqual(100);
-  expect(s.featureCount).toEqual(10);
-  expect((0, _stats.rectifyStats)({
-    featureCount: 3,
-    scoreSum: 6,
-    scoreSumSquares: 14
-  }).scoreStdDev).toEqual(1); // calculated from a webapp about sample standard deviations
-});
-test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var ret;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          _context.next = 2;
-          return (0, _stats.scoresToStats)({
-            refName: 'ctgA',
-            start: 0,
-            end: 2
-          }, (0, _rxjs.from)([new _simpleFeature.default({
-            id: 1,
-            data: {
-              start: 0,
-              end: 1,
-              score: 1
-            }
-          }), new _simpleFeature.default({
-            id: 2,
-            data: {
-              start: 1,
-              end: 2,
-              score: 2
-            }
-          }), new _simpleFeature.default({
-            id: 3,
-            data: {
-              start: 2,
-              end: 3,
-              score: 3
-            }
-          })]));
-
-        case 2:
-          ret = _context.sent;
-          expect(ret.scoreMean).toEqual(2);
-          expect(ret.featureDensity).toEqual(1);
-          expect(ret.scoreMax).toEqual(3);
-          expect(ret.scoreMin).toEqual(1);
-          expect(ret.scoreStdDev).toEqual(1); // calculated from a webapp
-
-        case 8:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-}))); // peter TODO: fix this test
-
-test('calc per base stats', function () {
-  // one score at start
-  expect((0, _stats.calcPerBaseStats)({
-    refName: 'ctgA',
-    start: 0,
-    end: 9
-  }, [new _simpleFeature.default({
-    id: 1,
-    data: {
-      start: 0,
-      end: 1,
-      score: 10
-    }
-  })])).toEqual([10, 0, 0, 0, 0, 0, 0, 0, 0]); // multiple features
-
-  expect((0, _stats.calcPerBaseStats)({
-    refName: 'ctgA',
-    start: 0,
-    end: 9
-  }, [new _simpleFeature.default({
-    id: 1,
-    data: {
-      start: 0,
-      end: 1,
-      score: 10
-    }
-  }), new _simpleFeature.default({
-    id: 2,
-    data: {
-      start: 8,
-      end: 9,
-      score: 10
-    }
-  })])).toEqual([10, 0, 0, 0, 0, 0, 0, 0, 10]); // multiple features
-
-  expect((0, _stats.calcPerBaseStats)({
-    refName: 'ctgA',
-    start: 15,
-    end: 30
-  }, [new _simpleFeature.default({
-    id: 1,
-    data: {
-      start: 10,
-      end: 20,
-      score: 10
-    }
-  }), new _simpleFeature.default({
-    id: 2,
-    data: {
-      start: 25,
-      end: 26,
-      score: 10
-    }
-  })])).toEqual([10, 10, 10, 10, 10, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0]); // feature starts before region
-
-  expect((0, _stats.calcPerBaseStats)({
-    refName: 'ctgA',
-    start: 10,
-    end: 19
-  }, [new _simpleFeature.default({
-    id: 1,
-    data: {
-      start: 5,
-      end: 15,
-      score: 10
-    }
-  }), new _simpleFeature.default({
-    id: 1,
-    data: {
-      start: 18,
-      end: 26,
-      score: 10
-    }
-  })])).toEqual([10, 10, 10, 10, 10, 0, 0, 0, 10]);
-});