@jbrowse/plugin-sequence 1.6.9 → 1.7.3

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,7 +1,7 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class extends IndexedFasta {
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-}
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends IndexedFasta {
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+}

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -0,0 +1,70 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+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 _indexedfasta = require("@gmod/indexedfasta");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _IndexedFastaAdapter = _interopRequireDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
+
+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; } }
+
+var _default = /*#__PURE__*/function (_IndexedFasta) {
+  (0, _inherits2["default"])(_default, _IndexedFasta);
+
+  var _super = _createSuper(_default);
+
+  function _default(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
+    var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
+    var gziLocation = (0, _configuration.readConfObject)(config, 'gziLocation');
+
+    if (!fastaLocation) {
+      throw new Error('must provide fastaLocation');
+    }
+
+    if (!faiLocation) {
+      throw new Error('must provide faiLocation');
+    }
+
+    if (!gziLocation) {
+      throw new Error('must provide gziLocation');
+    }
+
+    var fastaOpts = {
+      fasta: (0, _io.openLocation)(fastaLocation, _this.pluginManager),
+      fai: (0, _io.openLocation)(faiLocation, _this.pluginManager),
+      gzi: (0, _io.openLocation)(gziLocation, _this.pluginManager)
+    };
+    _this.fasta = new _indexedfasta.BgzipIndexedFasta(fastaOpts);
+    return _this;
+  }
+
+  return (0, _createClass2["default"])(_default);
+}(_IndexedFastaAdapter["default"]);
+
+exports["default"] = _default;

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.test.js

@@ -0,0 +1,64 @@
+"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 _BgzipFastaAdapter = _interopRequireDefault(require("./BgzipFastaAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('can use a indexed fasta with gzi', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, features, featuresArray, features2, featuresArray2;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _BgzipFastaAdapter["default"](_configSchema["default"].create({
+            fastaLocation: {
+              localPath: require.resolve('../../test_data/volvox.fa.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            faiLocation: {
+              localPath: require.resolve('../../test_data/volvox.fa.gz.fai'),
+              locationType: 'LocalPathLocation'
+            },
+            gziLocation: {
+              localPath: require.resolve('../../test_data/volvox.fa.gz.gzi'),
+              locationType: 'LocalPathLocation'
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context.sent;
+          expect(featuresArray).toMatchSnapshot();
+          features2 = adapter.getFeatures({
+            refName: 'ctgC',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 9;
+          return features2.pipe((0, _operators.toArray)()).toPromise();
+
+        case 9:
+          featuresArray2 = _context.sent;
+          expect(featuresArray2).toMatchSnapshot();
+
+        case 11:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));

package/dist/BgzipFastaAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/BgzipFastaAdapter/configSchema.js

@@ -0,0 +1,36 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('BgzipFastaAdapter', {
+  fastaLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/seq.fa.gz',
+      locationType: 'UriLocation'
+    }
+  },
+  faiLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/seq.fa.gz.fai',
+      locationType: 'UriLocation'
+    }
+  },
+  gziLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/seq.fa.gz.gzi',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/BgzipFastaAdapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/BgzipFastaAdapter/index.js

@@ -0,0 +1,15 @@
+"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"));

package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,19 +1,19 @@
-import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Instance } from 'mobx-state-tree';
-import MyConfigSchema from './configSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class extends BaseAdapter implements RegionsAdapter {
-    protected refSeqs: Promise<Record<string, number>>;
-    protected source: string;
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    private init;
-    getRegions(): Promise<{
-        refName: string;
-        start: number;
-        end: number;
-    }[]>;
-    getFeatures(): void;
-    getHeader(): {};
-    freeResources(): void;
-}
+import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Instance } from 'mobx-state-tree';
+import MyConfigSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseAdapter implements RegionsAdapter {
+    protected refSeqs: Promise<Record<string, number>>;
+    protected source: string;
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    private init;
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    getFeatures(): void;
+    getHeader(): {};
+    freeResources(): void;
+}

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -0,0 +1,170 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = 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 _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+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; } }
+
+var _default = /*#__PURE__*/function (_BaseAdapter) {
+  (0, _inherits2["default"])(_default, _BaseAdapter);
+
+  var _super = _createSuper(_default);
+
+  // the map of refSeq to length
+  function _default(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "refSeqs", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "source", void 0);
+    var chromSizesLocation = (0, _configuration.readConfObject)(config, 'chromSizesLocation');
+
+    if (!chromSizesLocation) {
+      throw new Error('must provide chromSizesLocation');
+    }
+
+    var file = (0, _io.openLocation)(chromSizesLocation, _this.pluginManager);
+    _this.source = file.toString();
+    _this.refSeqs = _this.init(file);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "init",
+    value: function () {
+      var _init = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(file) {
+        var data, refSeqs;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                _context.next = 2;
+                return file.readFile('utf8');
+
+              case 2:
+                data = _context.sent;
+                refSeqs = {};
+
+                if (data.length) {
+                  _context.next = 6;
+                  break;
+                }
+
+                throw new Error("Could not read file ".concat(file.toString()));
+
+              case 6:
+                data.split('\n').forEach(function (line) {
+                  if (line.length) {
+                    var _line$split = line.split('\t'),
+                        _line$split2 = (0, _slicedToArray2["default"])(_line$split, 2),
+                        name = _line$split2[0],
+                        length = _line$split2[1];
+
+                    refSeqs[name] = +length;
+                  }
+                });
+                return _context.abrupt("return", refSeqs);
+
+              case 8:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee);
+      }));
+
+      function init(_x) {
+        return _init.apply(this, arguments);
+      }
+
+      return init;
+    }()
+  }, {
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var refSeqs;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.refSeqs;
+
+              case 2:
+                refSeqs = _context2.sent;
+                return _context2.abrupt("return", Object.keys(refSeqs).map(function (refName) {
+                  return {
+                    refName: refName,
+                    start: 0,
+                    end: refSeqs[refName]
+                  };
+                }));
+
+              case 4:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRegions() {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures() {
+      throw new Error('sequence not available');
+    }
+  }, {
+    key: "getHeader",
+    value: function getHeader() {
+      return {};
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter2.BaseAdapter);
+
+exports["default"] = _default;

package/dist/ChromSizesAdapter/ChromSizesAdapter.test.js

@@ -0,0 +1,46 @@
+"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 _ChromSizesAdapter = _interopRequireDefault(require("./ChromSizesAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch sequence from volvox.chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, regions;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _ChromSizesAdapter["default"](_configSchema["default"].create({
+            chromSizesLocation: {
+              localPath: require.resolve('./test_data/volvox.chrom.sizes'),
+              locationType: 'LocalPathLocation'
+            }
+          }));
+          _context.next = 3;
+          return adapter.getRegions();
+
+        case 3:
+          regions = _context.sent;
+          expect(regions).toEqual([{
+            refName: 'ctgA',
+            start: 0,
+            end: 50001
+          }, {
+            refName: 'ctgB',
+            start: 0,
+            end: 6079
+          }]);
+
+        case 5:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));

package/dist/ChromSizesAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/ChromSizesAdapter/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 _default = (0, _configuration.ConfigurationSchema)('ChromSizesAdapter', {
+  chromSizesLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/species.chrom.sizes',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/ChromSizesAdapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/ChromSizesAdapter/index.js

@@ -0,0 +1,15 @@
+"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"));

package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -1,21 +1,21 @@
-/// <reference types="react" />
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Region } from '@jbrowse/core/util/types';
-interface MyProps {
-    exportSVG?: {
-        rasterizeLayers: boolean;
-    };
-    features: Map<string, Feature>;
-    regions: Region[];
-    bpPerPx: number;
-    config: AnyConfigurationModel;
-    highResolutionScaling: number;
-    theme: any;
-    showForward: boolean;
-    showReverse: boolean;
-    showTranslation: boolean;
-}
-declare function Sequence(props: MyProps): JSX.Element;
-declare const _default: typeof Sequence;
-export default _default;
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region } from '@jbrowse/core/util/types';
+interface MyProps {
+    exportSVG?: {
+        rasterizeLayers: boolean;
+    };
+    features: Map<string, Feature>;
+    regions: Region[];
+    bpPerPx: number;
+    config: AnyConfigurationModel;
+    highResolutionScaling: number;
+    theme: any;
+    showForward: boolean;
+    showReverse: boolean;
+    showTranslation: boolean;
+}
+declare function Sequence(props: MyProps): JSX.Element;
+declare const _default: typeof Sequence;
+export default _default;