@jbrowse/plugin-comparative-adapters 2.16.1 → 2.18.0

package/dist/DeltaAdapter/configSchema.js

@@ -1,41 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DeltaAdapter = (0, configuration_1.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/dist/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/dist/DeltaAdapter/util.js

@@ -1,34 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_delta2paf = paf_delta2paf;
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
-/* 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.
- */
 function paf_delta2paf(buffer) {
     let rname = '';
     let qname = '';
@@ -46,13 +18,14 @@ function paf_delta2paf(buffer) {
     const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
     let blockStart = 0;
     let i = 0;
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        const line = decoder.decode(b).trim();
         blockStart = n + 1;
         i++;
         if (line) {
@@ -125,7 +98,7 @@ function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 2);
-                    } // deletion
+                    }
                 }
                 else {
                     const l = -d - 1;
@@ -139,7 +112,7 @@ function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 1);
-                    } // insertion
+                    }
                 }
             }
         }

package/dist/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/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 +1,16 @@
-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<import("../PAFAdapter/util").PAFRecord[]>;
+    setupPre(opts?: BaseOptions): Promise<{
+        tname: string;
+        tstart: number;
+        tend: number;
+        qname: string;
+        qstart: number;
+        qend: number;
+        strand: number;
+        extra: {
+            mappingQual: number;
+        };
+    }[]>;
 }

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -3,16 +3,14 @@ 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 bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 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 {
     async setupPre(opts) {
         const outLoc = (0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager);
-        const buffer = (await outLoc.readFile(opts));
-        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)(outLoc, opts);
         return (0, util_2.parseLineByLine)(buf, parseMashMapLine);
     }
 }
@@ -20,7 +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

@@ -3,15 +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 bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 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");
@@ -29,14 +27,10 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async setupPre(opts) {
         const pm = this.pluginManager;
         const pafLocation = (0, io_1.openLocation)(this.getConf('pafLocation'), pm);
-        const buffer = (await pafLocation.readFile(opts));
-        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = await (0, util_1.fetchAndMaybeUnzip)(pafLocation, opts);
         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() {
@@ -50,7 +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);
@@ -68,18 +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`);
@@ -147,7 +134,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = PAFAdapter;