@jbrowse/plugin-comparative-adapters 2.17.0 → 2.18.0

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -1,8 +1,7 @@
-import { openLocation } from '@jbrowse/core/util/io';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
-// locals
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
 import { paf_delta2paf } from './util';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);

package/esm/DeltaAdapter/configSchema.d.ts

@@ -1,33 +1,19 @@
 declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: string;
         defaultValue: {

package/esm/DeltaAdapter/configSchema.js

@@ -1,39 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DeltaAdapter = ConfigurationSchema('DeltaAdapter', {
-    /**
-     * #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
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/DeltaAdapter/index.d.ts

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

package/esm/DeltaAdapter/util.js

@@ -1,30 +1,3 @@
-/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
- *
- * The MIT License
- *
- * Copyright (c) 2018-     Dana-Farber Cancer Institute
- *               2017-2018 Broad Institute, Inc.
- *
- * 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.
- */
 export function paf_delta2paf(buffer) {
     let rname = '';
     let qname = '';
@@ -122,7 +95,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 2);
-                    } // deletion
+                    }
                 }
                 else {
                     const l = -d - 1;
@@ -136,7 +109,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 1);
-                    } // insertion
+                    }
                 }
             }
         }

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 interface BareFeature {
     strand: number;
     refName: string;
@@ -24,11 +25,6 @@ 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/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2 } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { doesIntersect2, SimpleFeature, } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { readFile, parseBed } from '../util';
+import { parseBed, readFile } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
@@ -40,9 +40,6 @@ class MCScanAnchorsAdapter extends 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() {
@@ -51,7 +48,6 @@ class MCScanAnchorsAdapter extends 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);
@@ -68,8 +64,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return 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;
@@ -82,8 +76,6 @@ class MCScanAnchorsAdapter extends 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,
@@ -98,12 +90,7 @@ class MCScanAnchorsAdapter extends 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'];
 export default MCScanAnchorsAdapter;

package/esm/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/esm/MCScanAnchorsAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MCScanAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -14,9 +8,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -24,9 +15,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -34,9 +22,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/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/esm/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/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -1,9 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { openLocation } from '@jbrowse/core/util/io';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { doesIntersect2 } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { readFile, parseBed } from '../util';
+import { parseBed, readFile } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
@@ -51,9 +51,6 @@ class MCScanAnchorsAdapter extends 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() {
@@ -62,7 +59,6 @@ class MCScanAnchorsAdapter extends 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);
@@ -86,8 +82,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return 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;
@@ -127,12 +121,7 @@ class MCScanAnchorsAdapter extends 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'];
 export default MCScanAnchorsAdapter;

package/esm/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/esm/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MCScanSimpleAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanSimpleAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -14,9 +8,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -24,9 +15,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -34,9 +22,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/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/esm/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/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,5 +1,5 @@
-import { openLocation } from '@jbrowse/core/util/io';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { parseLineByLine } from '../util';
 export default class MashMapAdapter extends PAFAdapter {
@@ -12,7 +12,6 @@ export default class MashMapAdapter extends PAFAdapter {
 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/esm/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/esm/MashMapAdapter/configSchema.js

@@ -1,36 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MashMapAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MashMapAdapter = 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/esm/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/esm/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/esm/PAFAdapter/PAFAdapter.js

@@ -1,13 +1,12 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
+import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
-import { readConfObject, } from '@jbrowse/core/configuration';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-// locals
 import SyntenyFeature from '../SyntenyFeature';
-import { flipCigar, swapIndelCigar, parsePAFLine, parseLineByLine, } from '../util';
+import { flipCigar, parseLineByLine, parsePAFLine, swapIndelCigar, } from '../util';
 import { getWeightedMeans } from './util';
 const { parseCigar } = MismatchParser;
 class PAFAdapter extends BaseFeatureDataAdapter {
@@ -27,9 +26,6 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return parseLineByLine(buf, 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() {
@@ -43,7 +39,6 @@ class PAFAdapter extends 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);
@@ -61,18 +56,12 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return 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 && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
                 pafRecords = 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`);
@@ -140,7 +129,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;