@jbrowse/plugin-comparative-adapters 2.17.0 → 2.18.0

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_2 = require("../util");
 class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -42,9 +42,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures so is not
-        // really that important, and has to be true or else getFeatures is never
-        // called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -53,7 +50,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -70,8 +66,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -84,8 +78,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                             ...f1,
                             uniqueId: `${index}-${rowNum}`,
                             syntenyId: rowNum,
-                            // note: strand would be -1 if the two features are on opposite
-                            // strands, indicating inverted alignment
                             strand: f1.strand * f2.strand,
                             assemblyName: assemblyNames[+!flip],
                             score,
@@ -100,12 +92,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;

package/dist/MCScanAnchorsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed1Location: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed2Location: {
         type: string;
         defaultValue: {
@@ -29,9 +20,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/dist/MCScanAnchorsAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config MCScanAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +10,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -26,9 +17,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -36,9 +24,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/dist/MCScanAnchorsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MCScanAnchorsAdapterF(pluginManager: PluginManager): void;

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 interface BareFeature {
     refName: string;
     start: number;
@@ -32,11 +33,6 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }
 export {};

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const util_2 = require("../util");
@@ -56,9 +56,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures
-        // so is not really that important, and has to be true or else
-        // getFeatures is never called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -67,7 +64,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -91,8 +87,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -132,12 +126,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     mcscanSimpleAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed1Location: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed2Location: {
         type: string;
         defaultValue: {
@@ -29,9 +20,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/dist/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config MCScanSimpleAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanSimpleAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanSimpleAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +10,6 @@ const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCS
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -26,9 +17,6 @@ const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCS
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -36,9 +24,6 @@ const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCS
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/dist/MCScanSimpleAnchorsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MCScanSimpleAnchorsAdapterF(pluginManager: PluginManager): void;

package/dist/MashMapAdapter/MashMapAdapter.d.ts

@@ -1,5 +1,5 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class MashMapAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         tname: string;

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 const util_2 = require("../util");
 class MashMapAdapter extends PAFAdapter_1.default {
@@ -18,7 +18,6 @@ exports.default = MashMapAdapter;
 function parseMashMapLine(line) {
     const fields = line.split(' ');
     if (fields.length < 9) {
-        // xref https://github.com/marbl/MashMap/issues/38
         throw new Error(`improperly formatted line: ${line}`);
     }
     const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;

package/dist/MashMapAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const MashMapAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     outLocation: {
         type: string;
         defaultValue: {

package/dist/MashMapAdapter/configSchema.js

@@ -1,38 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config MashMapAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MashMapAdapter = (0, configuration_1.ConfigurationSchema)('MashMapAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the target assembly',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the query assembly',
     },
-    /**
-     * #slot
-     */
     outLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/MashMapAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MashMapAdapterF(pluginManager: PluginManager): void;

package/dist/PAFAdapter/PAFAdapter.d.ts

@@ -1,8 +1,9 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { PAFRecord } from './util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { PAFRecord } from './util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }

package/dist/PAFAdapter/PAFAdapter.js

@@ -3,14 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const range_1 = require("@jbrowse/core/util/range");
+const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
+const range_1 = require("@jbrowse/core/util/range");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-// locals
 const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
 const util_2 = require("../util");
 const util_3 = require("./util");
@@ -32,9 +31,6 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, util_2.parseLineByLine)(buf, util_2.parsePAFLine);
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures so is not
-        // really that important, and has to be true or else getFeatures is never
-        // called (BaseAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -48,7 +44,6 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const feats = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -66,18 +61,12 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             let pafRecords = await this.setup(opts);
             const { config } = opts;
-            // note: this is not the adapter config, it is responding to a display
-            // setting passed in via the opts parameter
             if (config && (0, configuration_1.readConfObject)(config, 'colorBy') === 'meanQueryIdentity') {
                 pafRecords = (0, util_3.getWeightedMeans)(pafRecords);
             }
             const assemblyNames = this.getAssemblyNames();
-            // The index of the assembly name in the query list corresponds to the
-            // adapter in the subadapters list
             const { start: qstart, end: qend, refName: qref, assemblyName } = query;
             const index = assemblyNames.indexOf(assemblyName);
-            // if the getFeatures::query is on the query assembly, flip orientation
-            // of data
             const flip = index === 0;
             if (index === -1) {
                 console.warn(`${assemblyName} not found in this adapter`);
@@ -145,7 +134,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = PAFAdapter;

package/dist/PAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pafLocation: {
         type: string;
         defaultValue: {

package/dist/PAFAdapter/configSchema.js

@@ -1,38 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config PAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PAFAdapter = (0, configuration_1.ConfigurationSchema)('PAFAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pafLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/PAFAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function PAFAdapterF(pluginManager: PluginManager): void;

package/dist/PAFAdapter/util.js

@@ -2,40 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getWeightedMeans = getWeightedMeans;
 const util_1 = require("../util");
-// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
-// License reproduced here
-//
-// MIT License
-// Copyright (c) 2017 Tom Poorten
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// The above copyright notice and this permission notice shall be included in all
-// copies or substantial portions of the Software.
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-//
-// Notes: in the weighted mean longer alignments factor in more heavily of all
-// the fragments of a query vs the reference that it mapped to
-//
-// this uses a combined key query+'-'+ref to iteratively map all the alignments
-// that match a particular ref from a particular query (so 1d array of what
-// could be a 2d map)
-//
-// the result is a single number that says e.g. chr5 from human mapped to chr5
-// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
-// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
-// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
-// this can show strong and weak levels of synteny, especially in polyploidy
-// situations
 function getWeightedMeans(ret) {
     const scoreMap = {};
     for (const entry of ret) {
@@ -70,7 +36,6 @@ function getWeightedMeans(ret) {
     }
     return ret;
 }
-// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import PluginManager from '@jbrowse/core/PluginManager';
 import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }