@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/BamAdapter/index.js

@@ -0,0 +1,36 @@
+"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"));
+
+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: 'BamAdapter',
+      configSchema: _configSchema["default"],
+      getAdapterClass: function getAdapterClass() {
+        return Promise.resolve().then(function () {
+          return _interopRequireWildcard(require('./BamAdapter'));
+        }).then(function (r) {
+          return r["default"];
+        });
+      }
+    });
+  });
+};
+
+exports["default"] = _default;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,43 +1,52 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-interface Header {
-    idToName?: string[];
-    nameToId?: Record<string, number>;
-    readGroups?: number[];
-}
-export default class CramAdapter extends BaseFeatureDataAdapter {
-    samHeader: Header;
-    private setupP?;
-    private seqIdToRefName;
-    private seqIdToOriginalRefName;
-    configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
-    }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
-    private seqFetch;
-    private setupPre;
-    private setup;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    refNameToId(refName: string): number | undefined;
-    refIdToName(refId: number): string | undefined;
-    refIdToOriginalName(refId: number): string;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
-        fetchSizeLimit: any;
-    }>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
-    private bytesForRegions;
-}
-export {};
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+interface Header {
+    idToName?: string[];
+    nameToId?: Record<string, number>;
+    readGroups?: number[];
+}
+export default class CramAdapter extends BaseFeatureDataAdapter {
+    samHeader: Header;
+    private setupP?;
+    private seqIdToRefName;
+    private seqIdToOriginalRefName;
+    configure(): Promise<{
+        cram: any;
+        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private seqFetch;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    refNameToId(refName: string): number | undefined;
+    refIdToName(refId: number): string | undefined;
+    refIdToOriginalName(refId: number): string;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: {
+            flagInclude: number;
+            flagExclude: number;
+            tagFilter: {
+                tag: string;
+                value: unknown;
+            };
+            name: string;
+        };
+    }): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+        bytes: any;
+        fetchSizeLimit: any;
+    }>;
+    /**
+     * get the approximate number of bytes queried from the file for the given
+     * query regions
+     * @param regions - list of query regions
+     */
+    private bytesForRegions;
+}
+export {};