@jbrowse/plugin-comparative-adapters 2.17.0 → 2.18.0

package/dist/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -1,109 +1,55 @@
-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 BlastColumns {
-    /** Query Seq-id */
     qseqid?: string;
-    /** Query GI */
     qgi?: string;
-    /** Query accesion */
     qacc?: string;
-    /** Subject Seq-id */
     sseqid?: string;
-    /** All subject Seq-id(s), separated by a ';' */
     sallseqid?: string;
-    /** Subject GI */
     sgi?: string;
-    /** All subject GIs */
     sallgi?: string;
-    /** Subject accession */
     sacc?: string;
-    /** All subject accessions */
     sallacc?: string;
-    /** Start of alignment in query */
     qstart?: number;
-    /** End of alignment in query */
     qend?: number;
-    /** Start of alignment in subject */
     sstart?: number;
-    /** End of alignment in subject */
     send?: number;
-    /** Aligned part of query sequence */
     qseq?: string;
-    /** Aligned part of subject sequence */
     sseq?: string;
-    /** Expect value */
     evalue?: string;
-    /** Bit score */
     bitscore?: string;
-    /** Raw score */
     score?: string;
-    /** Alignment length */
     length?: string;
-    /** Percentage of identical matches */
     pident?: string;
-    /** Number of identical matches */
     nident?: string;
-    /** Number of mismatches */
     mismatch?: string;
-    /** Number of positive-scoring matches */
     positive?: string;
-    /** Number of gap openings */
     gapopen?: string;
-    /** Total number of gap */
     gaps?: string;
-    /** Percentage of positive-scoring matches */
     ppos?: string;
-    /** Query and subject frames separated by a '/' */
     frames?: string;
-    /** Query frame */
     qframe?: string;
-    /** Subject frame */
     sframe?: string;
-    /** Blast traceback operations (BTOP) */
     btop?: string;
-    /** Unique Subject Taxonomy ID(s), separated by a ';'(in numerical order) */
     staxids?: string;
-    /** Unique Subject Scientific Name(s), separated by a ';' */
     sscinames?: string;
-    /** Unique Subject Common Name(s), separated by a ';' */
     scomnames?: string;
-    /**
-     * Unique Subject Blast Name(s), separated by a ';' (in alphabetical order)
-     */
     sblastnames?: string;
-    /**
-     * Unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)
-     */
     sskingdoms?: string;
-    /** Subject Title */
     stitle?: string;
-    /** All Subject Title(s), separated by a '<>' */
     salltitles?: string;
-    /** Subject Strand */
     sstrand?: string;
-    /** Query Coverage Per Subject (for all HSPs) */
     qcovs?: string;
-    /** Query Coverage Per HSP */
     qcovhsp?: string;
-    /**
-     * A measure of Query Coverage that counts a position in a subject sequence
-     * for this measure only once. The second time the position is aligned to the
-     * query is not counted towards this measure.
-     */
     qcovus?: string;
 }
 interface BlastRecord extends BlastColumns {
-    /** Query Seq-id */
     qseqid: string;
-    /** Subject Seq-id */
     sseqid: string;
-    /** Start of alignment in query */
     qstart: number;
-    /** End of alignment in query */
     qend: number;
-    /** Start of alignment in subject */
     sstart: number;
-    /** End of alignment in subject */
     send: number;
 }
 export default class BlastTabularAdapter extends BaseFeatureDataAdapter {

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -5,11 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
-const util_2 = require("../util");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
+const util_2 = require("../util");
 function createBlastLineParser(columns) {
     const columnNames = columns.trim().split(' ');
     const qseqidIndex = columnNames.indexOf('qseqid');
@@ -68,7 +68,6 @@ function createBlastLineParser(columns) {
             if (!value) {
                 continue;
             }
-            // @ts-expect-error
             record[columnName] = value;
         }
         return record;
@@ -91,9 +90,6 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, util_2.parseLineByLine)(buf, createBlastLineParser(columns));
     }
     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() {
@@ -107,7 +103,6 @@ class BlastTabularAdapter 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.getData(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -125,8 +120,6 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const blastRecords = await this.getData(opts);
             const [queryAssembly, targetAssembly] = this.getAssemblyNames();
-            // The index of the assembly name in the query list corresponds to the
-            // adapter in the subadapters list
             const { refName: queryRefName, assemblyName: queryAssemblyName, start: queryStart, end: queryEnd, } = query;
             if (queryAssemblyName !== targetAssembly &&
                 queryAssemblyName !== queryAssembly) {
@@ -201,7 +194,7 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BlastTabularAdapter;

package/dist/BlastTabularAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const BlastTabularAdapter: 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
-     */
     blastTableLocation: {
         type: string;
         defaultValue: {
@@ -33,9 +21,6 @@ declare const BlastTabularAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columns: {
         type: string;
         description: string;

package/dist/BlastTabularAdapter/configSchema.js

@@ -1,38 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BlastTabularAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BlastTabularAdapter = (0, configuration_1.ConfigurationSchema)('BlastTabularAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Query assembly is the first value in the array, target assembly 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
-     */
     blastTableLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -40,9 +25,6 @@ const BlastTabularAdapter = (0, configuration_1.ConfigurationSchema)('BlastTabul
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     columns: {
         type: 'string',
         description: 'Optional space-separated column name list. If custom columns were used in outfmt, enter them here exactly as specified in the command. At least qseqid, sseqid, qstart, qend, sstart, and send are required',

package/dist/BlastTabularAdapter/index.d.ts

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

package/dist/ChainAdapter/ChainAdapter.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 ChainAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         qname: string;

package/dist/ChainAdapter/ChainAdapter.js

@@ -3,11 +3,10 @@ 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");
-// locals
-const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
+const io_1 = require("@jbrowse/core/util/io");
 const util_2 = require("./util");
+const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class ChainAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('chainLocation'), this.pluginManager);

package/dist/ChainAdapter/configSchema.d.ts

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

package/dist/ChainAdapter/configSchema.js

@@ -1,41 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config ChainAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ChainAdapter = (0, configuration_1.ConfigurationSchema)('ChainAdapter', {
-    /**
-     * #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
-     * can be specified as alternative to assemblyNames
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the target assembly',
     },
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the query assembly',
     },
-    /**
-     * #slot
-     */
     chainLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },

package/dist/ChainAdapter/index.d.ts

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

package/dist/ChainAdapter/util.js

@@ -1,30 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_chain2paf = paf_chain2paf;
-/* adapted from chain2paf by Andrea Guarracino, license reproduced below
- *
- * MIT License
- *
- * Copyright (c) 2021 Andrea Guarracino
- *
- * 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 generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
     return {
         qname,
@@ -64,26 +40,12 @@ function paf_chain2paf(buffer) {
         const b = buffer.subarray(blockStart, n);
         const l = decoder.decode(b).trim();
         blockStart = n + 1;
-        const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
+        const l_tab = l.replaceAll(' ', '\t');
         const l_vec = l_tab.split('\t');
         if (l_vec[0] === 'chain') {
-            // Emit previous PAF row, if available
             if (cigar) {
                 records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
             }
-            // Save query/target information
-            // score -- chain score
-            // tName -- chromosome (reference sequence)
-            // tSize -- chromosome size (reference sequence)
-            // tStrand -- strand (reference sequence)
-            // tStart -- alignment start position (reference sequence)
-            // tEnd -- alignment end position (reference sequence)
-            // qName -- chromosome (query sequence)
-            // qSize -- chromosome size (query sequence)
-            // qStrand -- strand (query sequence)
-            // qStart -- alignment start position (query sequence)
-            // qEnd -- alignment end position (query sequence)
-            // id -- chain ID
             t_name = l_vec[2];
             t_start = +l_vec[5];
             t_end = +l_vec[6];
@@ -97,18 +59,10 @@ function paf_chain2paf(buffer) {
                 q_start = +q_size - q_end;
                 q_end = +q_size - tmp;
             }
-            // Initialize PAF fields
             num_matches = 0;
             cigar = '';
         }
         else {
-            // size -- the size of the ungapped alignment
-            //
-            // dt -- the difference between the end of this block and the beginning
-            //    of the next block (reference sequence)
-            //
-            // dq -- the difference between the end of this block and the beginning
-            //    of the next block (query sequence)
             const size_ungapped_alignment = +l_vec[0] || 0;
             const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
@@ -124,7 +78,6 @@ function paf_chain2paf(buffer) {
             }
         }
     }
-    // Emit last PAF row, if available
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }

package/dist/DeltaAdapter/DeltaAdapter.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 DeltaAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         qname: string;

package/dist/DeltaAdapter/DeltaAdapter.js

@@ -3,11 +3,10 @@ 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");
-// locals
-const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
+const io_1 = require("@jbrowse/core/util/io");
 const util_2 = require("./util");
+const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class DeltaAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager);

package/dist/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/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

@@ -1,33 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_delta2paf = paf_delta2paf;
-/* 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 = '';
@@ -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 {};