@jbrowse/plugin-comparative-adapters 2.13.1 → 2.15.0

package/dist/ChainAdapter/ChainAdapter.js

@@ -4,18 +4,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const io_1 = require("@jbrowse/core/util/io");
+const util_1 = require("@jbrowse/core/util");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
-const util_1 = require("./util");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+const util_2 = require("./util");
 class ChainAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('chainLocation'), this.pluginManager);
         const buffer = (await loc.readFile(opts));
-        const buf = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
-        return (0, util_1.paf_chain2paf)(buf);
+        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        return (0, util_2.paf_chain2paf)(buf);
     }
 }
 exports.default = ChainAdapter;

package/dist/ChainAdapter/util.js

@@ -61,7 +61,7 @@ function paf_chain2paf(buffer) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const l = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         blockStart = n + 1;
         const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
@@ -114,13 +114,13 @@ function paf_chain2paf(buffer) {
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
             if (size_ungapped_alignment !== 0) {
                 num_matches += +size_ungapped_alignment;
-                cigar += size_ungapped_alignment + 'M';
+                cigar += `${size_ungapped_alignment}M`;
             }
             if (diff_in_query !== 0) {
-                cigar += diff_in_query + 'I';
+                cigar += `${diff_in_query}I`;
             }
             if (diff_in_target !== 0) {
-                cigar += diff_in_target + 'D';
+                cigar += `${diff_in_target}D`;
             }
         }
     }

package/dist/DeltaAdapter/DeltaAdapter.js

@@ -7,14 +7,12 @@ const io_1 = require("@jbrowse/core/util/io");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 const util_1 = require("./util");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+const util_2 = require("@jbrowse/core/util");
 class DeltaAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager);
         const buffer = (await loc.readFile(opts));
-        const buf = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = (0, util_2.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
         return (0, util_1.paf_delta2paf)(buf);
     }
 }

package/dist/DeltaAdapter/util.js

@@ -51,7 +51,7 @@ function paf_delta2paf(buffer) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         blockStart = n + 1;
         i++;
@@ -120,7 +120,6 @@ function paf_delta2paf(buffer) {
                     if (l > 0) {
                         cigar.push(l << 4);
                     }
-                    // eslint-disable-next-line unicorn/prefer-at
                     if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
                         cigar[cigar.length - 1] += 1 << 4;
                     }
@@ -135,7 +134,6 @@ function paf_delta2paf(buffer) {
                     if (l > 0) {
                         cigar.push(l << 4);
                     }
-                    // eslint-disable-next-line unicorn/prefer-at
                     if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
                         cigar[cigar.length - 1] += 1 << 4;
                     }

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -8,7 +8,7 @@ const util_2 = require("../util");
 class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -12,7 +12,7 @@ const util_2 = require("../util");
 class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -5,17 +5,15 @@ var __importDefault = (this && this.__importDefault) || function (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 PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
-const util_1 = require("../util");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+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 = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
-        return (0, util_1.parseLineByLine)(buf, parseMashMapLine);
+        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        return (0, util_2.parseLineByLine)(buf, parseMashMapLine);
     }
 }
 exports.default = MashMapAdapter;
@@ -23,14 +21,14 @@ 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);
+        throw new Error(`improperly formatted line: ${line}`);
     }
     const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;
     return {
-        tname,
+        tname: tname,
         tstart: +tstart,
         tend: +tend,
-        qname,
+        qname: qname,
         qstart: +qstart,
         qend: +qend,
         strand: strand === '-' ? -1 : 1,

package/dist/PAFAdapter/PAFAdapter.js

@@ -7,18 +7,19 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const range_1 = require("@jbrowse/core/util/range");
 const io_1 = require("@jbrowse/core/util/io");
 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_1 = require("../util");
-const util_2 = require("./util");
+const util_2 = require("../util");
+const util_3 = require("./util");
 const { parseCigar } = plugin_alignments_1.MismatchParser;
 class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });
@@ -30,7 +31,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         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;
-        return (0, util_1.parseLineByLine)(buf, util_1.parsePAFLine);
+        return (0, util_2.parseLineByLine)(buf, util_2.parsePAFLine);
     }
     async hasDataForRefName() {
         // determining this properly is basically a call to getFeatures
@@ -70,7 +71,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             // 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_2.getWeightedMeans)(pafRecords);
+                pafRecords = (0, util_3.getWeightedMeans)(pafRecords);
             }
             const assemblyNames = this.getAssemblyNames();
             // The index of the assembly name in the query list corresponds to the
@@ -114,10 +115,10 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     let CIGAR = extra.cg;
                     if (extra.cg) {
                         if (flip && strand === -1) {
-                            CIGAR = (0, util_1.flipCigar)(parseCigar(extra.cg)).join('');
+                            CIGAR = (0, util_2.flipCigar)(parseCigar(extra.cg)).join('');
                         }
                         else if (flip) {
-                            CIGAR = (0, util_1.swapIndelCigar)(extra.cg);
+                            CIGAR = (0, util_2.swapIndelCigar)(extra.cg);
                         }
                     }
                     observer.next(new SyntenyFeature_1.default({

package/dist/PAFAdapter/util.js

@@ -41,7 +41,7 @@ function getWeightedMeans(ret) {
     for (const entry of ret) {
         const query = entry.qname;
         const target = entry.tname;
-        const key = query + '-' + target;
+        const key = `${query}-${target}`;
         if (!scoreMap[key]) {
             scoreMap[key] = { quals: [], len: [] };
         }
@@ -55,7 +55,7 @@ function getWeightedMeans(ret) {
     for (const entry of ret) {
         const query = entry.qname;
         const target = entry.tname;
-        const key = query + '-' + target;
+        const key = `${query}-${target}`;
         entry.extra.meanScore = meanScoreMap[key];
     }
     let min = 10000;
@@ -72,7 +72,6 @@ function getWeightedMeans(ret) {
 }
 // https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
-    // eslint-disable-next-line unicorn/no-array-reduce
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,
         weightSum + weight,

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -41,8 +41,8 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return true;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        var _a, _b;
+        const r1 = (_b = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.assemblyName;
         if (!r1) {
             throw new Error('no assembly name provided');
         }
@@ -54,7 +54,9 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         else if (idx === 1) {
             return names.filter(n => n.startsWith('t')).map(n => n.slice(1));
         }
-        return [];
+        else {
+            return [];
+        }
     }
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {

package/dist/SyntenyFeature/index.js

@@ -5,7 +5,6 @@ const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 // locals
 const { getMismatches } = plugin_alignments_1.MismatchParser;
 class SyntenyFeature extends util_1.SimpleFeature {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(arg) {
         if (arg === 'mismatches') {
             return getMismatches(this.get('CIGAR'));

package/dist/util.d.ts

@@ -1,18 +1,17 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
 import { PAFRecord } from './PAFAdapter/util';
-export declare function isGzip(buf: Buffer): boolean;
-export declare function parseBed(text: string): Map<string, {
-    refName: string;
+export declare function parseBed(text: string): Map<string | undefined, {
+    refName: string | undefined;
     start: number;
     end: number;
     score: number;
-    name: string;
+    name: string | undefined;
     strand: number;
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
 export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];
 export declare function parsePAFLine(line: string): PAFRecord;
-export declare function flipCigar(cigar: string[]): string[];
+export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isGzip = isGzip;
 exports.parseBed = parseBed;
 exports.readFile = readFile;
 exports.zip = zip;
@@ -9,9 +8,7 @@ exports.parsePAFLine = parsePAFLine;
 exports.flipCigar = flipCigar;
 exports.swapIndelCigar = swapIndelCigar;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+const util_1 = require("@jbrowse/core/util");
 function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -33,7 +30,7 @@ function parseBed(text) {
 }
 async function readFile(file, opts) {
     const buffer = (await file.readFile(opts));
-    return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer);
+    return new TextDecoder('utf8', { fatal: true }).decode((0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer);
 }
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
@@ -47,7 +44,7 @@ function parseLineByLine(buffer, cb) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         if (line) {
             entries.push(cb(line));

package/esm/ChainAdapter/ChainAdapter.js

@@ -1,10 +1,8 @@
 import { openLocation } from '@jbrowse/core/util/io';
+import { isGzip } from '@jbrowse/core/util';
 import { unzip } from '@gmod/bgzf-filehandle';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_chain2paf } from './util';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 export default class ChainAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('chainLocation'), this.pluginManager);

package/esm/ChainAdapter/util.js

@@ -58,7 +58,7 @@ export function paf_chain2paf(buffer) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const l = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         blockStart = n + 1;
         const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
@@ -111,13 +111,13 @@ export function paf_chain2paf(buffer) {
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
             if (size_ungapped_alignment !== 0) {
                 num_matches += +size_ungapped_alignment;
-                cigar += size_ungapped_alignment + 'M';
+                cigar += `${size_ungapped_alignment}M`;
             }
             if (diff_in_query !== 0) {
-                cigar += diff_in_query + 'I';
+                cigar += `${diff_in_query}I`;
             }
             if (diff_in_target !== 0) {
-                cigar += diff_in_target + 'D';
+                cigar += `${diff_in_target}D`;
             }
         }
     }

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -2,9 +2,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { unzip } from '@gmod/bgzf-filehandle';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_delta2paf } from './util';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+import { isGzip } from '@jbrowse/core/util';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);

package/esm/DeltaAdapter/util.js

@@ -48,7 +48,7 @@ export function paf_delta2paf(buffer) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         blockStart = n + 1;
         i++;
@@ -117,7 +117,6 @@ export function paf_delta2paf(buffer) {
                     if (l > 0) {
                         cigar.push(l << 4);
                     }
-                    // eslint-disable-next-line unicorn/prefer-at
                     if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
                         cigar[cigar.length - 1] += 1 << 4;
                     }
@@ -132,7 +131,6 @@ export function paf_delta2paf(buffer) {
                     if (l > 0) {
                         cigar.push(l << 4);
                     }
-                    // eslint-disable-next-line unicorn/prefer-at
                     if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
                         cigar[cigar.length - 1] += 1 << 4;
                     }

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -6,7 +6,7 @@ import { readFile, parseBed } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -7,7 +7,7 @@ import { readFile, parseBed } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,10 +1,8 @@
 import { openLocation } from '@jbrowse/core/util/io';
 import { unzip } from '@gmod/bgzf-filehandle';
+import { isGzip } from '@jbrowse/core/util';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { parseLineByLine } from '../util';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 export default class MashMapAdapter extends PAFAdapter {
     async setupPre(opts) {
         const outLoc = openLocation(this.getConf('outLocation'), this.pluginManager);
@@ -17,14 +15,14 @@ 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);
+        throw new Error(`improperly formatted line: ${line}`);
     }
     const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;
     return {
-        tname,
+        tname: tname,
         tstart: +tstart,
         tend: +tend,
-        qname,
+        qname: qname,
         qstart: +qstart,
         qend: +qend,
         strand: strand === '-' ? -1 : 1,

package/esm/PAFAdapter/PAFAdapter.js

@@ -2,18 +2,19 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { isGzip } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { unzip } from '@gmod/bgzf-filehandle';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
 // locals
 import SyntenyFeature from '../SyntenyFeature';
-import { flipCigar, swapIndelCigar, parsePAFLine, isGzip, parseLineByLine, } from '../util';
+import { flipCigar, swapIndelCigar, parsePAFLine, parseLineByLine, } from '../util';
 import { getWeightedMeans } from './util';
 const { parseCigar } = MismatchParser;
 class PAFAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch(e => {
+            this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/PAFAdapter/util.js

@@ -38,7 +38,7 @@ export function getWeightedMeans(ret) {
     for (const entry of ret) {
         const query = entry.qname;
         const target = entry.tname;
-        const key = query + '-' + target;
+        const key = `${query}-${target}`;
         if (!scoreMap[key]) {
             scoreMap[key] = { quals: [], len: [] };
         }
@@ -52,7 +52,7 @@ export function getWeightedMeans(ret) {
     for (const entry of ret) {
         const query = entry.qname;
         const target = entry.tname;
-        const key = query + '-' + target;
+        const key = `${query}-${target}`;
         entry.extra.meanScore = meanScoreMap[key];
     }
     let min = 10000;
@@ -69,7 +69,6 @@ export function getWeightedMeans(ret) {
 }
 // https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
-    // eslint-disable-next-line unicorn/no-array-reduce
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,
         weightSum + weight,

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -36,8 +36,8 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return true;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        var _a, _b;
+        const r1 = (_b = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.assemblyName;
         if (!r1) {
             throw new Error('no assembly name provided');
         }
@@ -49,7 +49,9 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         else if (idx === 1) {
             return names.filter(n => n.startsWith('t')).map(n => n.slice(1));
         }
-        return [];
+        else {
+            return [];
+        }
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {

package/esm/SyntenyFeature/index.js

@@ -3,7 +3,6 @@ import { MismatchParser } from '@jbrowse/plugin-alignments';
 // locals
 const { getMismatches } = MismatchParser;
 export default class SyntenyFeature extends SimpleFeature {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(arg) {
         if (arg === 'mismatches') {
             return getMismatches(this.get('CIGAR'));

package/esm/util.d.ts

@@ -1,18 +1,17 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
 import { PAFRecord } from './PAFAdapter/util';
-export declare function isGzip(buf: Buffer): boolean;
-export declare function parseBed(text: string): Map<string, {
-    refName: string;
+export declare function parseBed(text: string): Map<string | undefined, {
+    refName: string | undefined;
     start: number;
     end: number;
     score: number;
-    name: string;
+    name: string | undefined;
     strand: number;
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
 export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];
 export declare function parsePAFLine(line: string): PAFRecord;
-export declare function flipCigar(cigar: string[]): string[];
+export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/esm/util.js

@@ -1,7 +1,5 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+import { isGzip } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -37,7 +35,7 @@ export function parseLineByLine(buffer, cb) {
         if (n === -1) {
             break;
         }
-        const b = buffer.slice(blockStart, n);
+        const b = buffer.subarray(blockStart, n);
         const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
         if (line) {
             entries.push(cb(line));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.13.1",
+  "version": "2.15.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/comparative-adapters",
+    "test": "cd ../..; jest --passWithNoTests plugins/comparative-adapters",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -44,7 +44,7 @@
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-alignments": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
-    "@mui/material": "^5.0.0",
+    "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }