@jbrowse/plugin-comparative-adapters 3.7.0 → 4.0.0

package/esm/PAFAdapter/util.js

@@ -1,42 +1,32 @@
-import { zip } from '../util';
 export function getWeightedMeans(ret) {
     const scoreMap = {};
     for (const entry of ret) {
-        const query = entry.qname;
-        const target = entry.tname;
-        const key = `${query}-${target}`;
-        if (!scoreMap[key]) {
-            scoreMap[key] = { quals: [], len: [] };
+        const key = `${entry.qname}-${entry.tname}`;
+        const qual = entry.extra.mappingQual || 1;
+        const len = entry.extra.blockLen || 1;
+        const existing = scoreMap[key];
+        if (existing) {
+            existing.valueSum += qual * len;
+            existing.weightSum += len;
+        }
+        else {
+            scoreMap[key] = { valueSum: qual * len, weightSum: len };
         }
-        scoreMap[key].quals.push(entry.extra.mappingQual || 1);
-        scoreMap[key].len.push(entry.extra.blockLen || 1);
     }
-    const meanScoreMap = Object.fromEntries(Object.entries(scoreMap).map(([key, val]) => {
-        const vals = zip(val.quals, val.len);
-        return [key, weightedMean(vals)];
-    }));
-    for (const entry of ret) {
-        const query = entry.qname;
-        const target = entry.tname;
-        const key = `${query}-${target}`;
-        entry.extra.meanScore = meanScoreMap[key];
+    const meanScoreMap = {};
+    let min = Infinity;
+    let max = -Infinity;
+    for (const [key, { valueSum, weightSum }] of Object.entries(scoreMap)) {
+        const mean = valueSum / weightSum;
+        meanScoreMap[key] = mean;
+        min = Math.min(mean, min);
+        max = Math.max(mean, max);
     }
-    let min = 10000;
-    let max = 0;
+    const range = max - min;
     for (const entry of ret) {
-        min = Math.min(entry.extra.meanScore || 0, min);
-        max = Math.max(entry.extra.meanScore || 0, max);
-    }
-    for (const entry of ret) {
-        const b = entry.extra.meanScore || 0;
-        entry.extra.meanScore = (b - min) / (max - min);
+        const key = `${entry.qname}-${entry.tname}`;
+        const score = meanScoreMap[key];
+        entry.extra.meanScore = range > 0 ? (score - min) / range : 1;
     }
     return ret;
 }
-function weightedMean(tuples) {
-    const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
-        valueSum + value * weight,
-        weightSum + weight,
-    ], [0, 0]);
-    return valueSum / weightSum;
-}

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -3,9 +3,11 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SyntenyFeature from '../SyntenyFeature';
-import { parsePAFLine } from '../util';
-class PAFAdapter extends BaseFeatureDataAdapter {
+import SyntenyFeature from "../SyntenyFeature/index.js";
+import { parsePAFLine } from "../util.js";
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames'];
+    pif;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const pifGzLoc = this.getConf('pifGzLocation');
@@ -36,8 +38,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return true;
     }
     async getRefNames(opts = {}) {
-        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;
+        const r1 = opts.regions?.[0]?.assemblyName;
         if (!r1) {
             throw new Error('no assembly name provided');
         }
@@ -61,17 +62,19 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             const index = assemblyNames.indexOf(assemblyName);
             const flip = index === 0;
             const letter = flip ? 'q' : 't';
+            const mateAssemblyName = assemblyNames[flip ? 1 : 0];
             await updateStatus('Downloading features', statusCallback, () => this.pif.getLines(letter + query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
                     const r = parsePAFLine(line);
-                    const refName = r.qname.slice(1);
+                    const { extra, strand } = r;
+                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
                     const start = r.qstart;
                     const end = r.qend;
+                    const refName = r.qname.slice(1);
                     const mateName = r.tname;
                     const mateStart = r.tstart;
                     const mateEnd = r.tend;
-                    const { extra, strand } = r;
-                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
+                    const CIGAR = extra.cg;
                     observer.next(new SyntenyFeature({
                         uniqueId: fileOffset + assemblyName,
                         assemblyName,
@@ -81,7 +84,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                         refName,
                         strand,
                         ...rest,
-                        CIGAR: extra.cg,
+                        CIGAR,
                         syntenyId: fileOffset,
                         identity: numMatches / blockLen,
                         numMatches,
@@ -90,7 +93,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                             start: mateStart,
                             end: mateEnd,
                             refName: mateName,
-                            assemblyName: assemblyNames[+flip],
+                            assemblyName: mateAssemblyName,
                         },
                     }));
                 },
@@ -100,5 +103,3 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         });
     }
 }
-PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default PAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const PairwiseIndexedPAFAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -22,9 +22,9 @@ declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/con
             locationType: string;
         };
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
@@ -35,6 +35,6 @@ declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/con
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PairwiseIndexedPAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter', {
     assemblyNames: {

package/esm/PairwiseIndexedPAFAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function PairwiseIndexedPAFAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'PairwiseIndexedPAFAdapter',
@@ -8,6 +8,6 @@ export default function PairwiseIndexedPAFAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./PairwiseIndexedPAFAdapter').then(r => r.default),
+        getAdapterClass: () => import("./PairwiseIndexedPAFAdapter.js").then(r => r.default),
     }));
 }

package/esm/SyntenyFeature/index.js

@@ -3,9 +3,8 @@ import { MismatchParser } from '@jbrowse/plugin-alignments';
 const { getMismatches } = MismatchParser;
 export default class SyntenyFeature extends SimpleFeature {
     get(arg) {
-        if (arg === 'mismatches') {
-            return getMismatches(this.get('CIGAR'));
-        }
-        return super.get(arg);
+        return arg === 'mismatches'
+            ? getMismatches(this.get('CIGAR'))
+            : super.get(arg);
     }
 }

package/esm/index.js

@@ -1,20 +1,17 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BlastTabularAdapter from './BlastTabularAdapter';
-import ChainAdapterF from './ChainAdapter';
-import ComparativeAddTrackComponentF from './ComparativeAddTrackComponent';
-import DeltaAdapterF from './DeltaAdapter';
-import GuessAdapterF from './GuessAdapter';
-import MCScanAddTrackComponentF from './MCScanAddTrackComponent';
-import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
-import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
-import MashMapAdapterF from './MashMapAdapter';
-import PAFAdapterF from './PAFAdapter';
-import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
+import BlastTabularAdapter from "./BlastTabularAdapter/index.js";
+import ChainAdapterF from "./ChainAdapter/index.js";
+import ComparativeAddTrackComponentF from "./ComparativeAddTrackComponent/index.js";
+import DeltaAdapterF from "./DeltaAdapter/index.js";
+import GuessAdapterF from "./GuessAdapter/index.js";
+import MCScanAddTrackComponentF from "./MCScanAddTrackComponent/index.js";
+import MCScanAnchorsAdapterF from "./MCScanAnchorsAdapter/index.js";
+import MCScanSimpleAnchorsAdapterF from "./MCScanSimpleAnchorsAdapter/index.js";
+import MashMapAdapterF from "./MashMapAdapter/index.js";
+import PAFAdapterF from "./PAFAdapter/index.js";
+import PairwiseIndexedPAFAdapterF from "./PairwiseIndexedPAFAdapter/index.js";
 export default class ComparativeAdaptersPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'ComparativeAdaptersPlugin';
-    }
+    name = 'ComparativeAdaptersPlugin';
     install(pluginManager) {
         PAFAdapterF(pluginManager);
         PairwiseIndexedPAFAdapterF(pluginManager);

package/esm/util.d.ts

@@ -1,4 +1,4 @@
-import type { PAFRecord } from './PAFAdapter/util';
+import type { PAFRecord } from './PAFAdapter/util.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseBed(text: string): Map<string | undefined, {

package/esm/util.js

@@ -2,7 +2,7 @@ import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
-        .filter(f => !!f || f.startsWith('#'))
+        .filter(f => !!f && !f.startsWith('#'))
         .map(line => {
         const [refName, start, end, name, score, strand] = line.split('\t');
         return [

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -15,48 +15,41 @@
     "directory": "plugins/comparative-adapters"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/comparative-adapters",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@gmod/tabix": "^3.0.1",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-alignments": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@mui/material": "^7.0.0",
-    "generic-filehandle2": "^2.0.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "@gmod/tabix": "^3.2.2",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.6",
+    "generic-filehandle2": "^2.0.18",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "rxjs": "^7.8.2",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-alignments": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/comparative-adapters",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -1,65 +0,0 @@
-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 {
-    qseqid?: string;
-    qgi?: string;
-    qacc?: string;
-    sseqid?: string;
-    sallseqid?: string;
-    sgi?: string;
-    sallgi?: string;
-    sacc?: string;
-    sallacc?: string;
-    qstart?: number;
-    qend?: number;
-    sstart?: number;
-    send?: number;
-    qseq?: string;
-    sseq?: string;
-    evalue?: string;
-    bitscore?: string;
-    score?: string;
-    length?: string;
-    pident?: string;
-    nident?: string;
-    mismatch?: string;
-    positive?: string;
-    gapopen?: string;
-    gaps?: string;
-    ppos?: string;
-    frames?: string;
-    qframe?: string;
-    sframe?: string;
-    btop?: string;
-    staxids?: string;
-    sscinames?: string;
-    scomnames?: string;
-    sblastnames?: string;
-    sskingdoms?: string;
-    stitle?: string;
-    salltitles?: string;
-    sstrand?: string;
-    qcovs?: string;
-    qcovhsp?: string;
-    qcovus?: string;
-}
-interface BlastRecord extends BlastColumns {
-    qseqid: string;
-    sseqid: string;
-    qstart: number;
-    qend: number;
-    sstart: number;
-    send: number;
-}
-export default class BlastTabularAdapter extends BaseFeatureDataAdapter {
-    private data;
-    static capabilities: string[];
-    getData(opts?: BaseOptions): Promise<BlastRecord[]>;
-    setup(opts?: BaseOptions): Promise<BlastRecord[]>;
-    hasDataForRefName(): Promise<boolean>;
-    getAssemblyNames(): string[];
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}
-export {};

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -1,206 +0,0 @@
-"use strict";
-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 util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
-function createBlastLineParser(columns) {
-    const columnNames = columns.trim().split(' ');
-    const qseqidIndex = columnNames.indexOf('qseqid');
-    if (qseqidIndex === -1) {
-        throw new Error('Missing required column "qseqid"');
-    }
-    const sseqidIndex = columnNames.indexOf('sseqid');
-    if (sseqidIndex === -1) {
-        throw new Error('Missing required column "sseqid"');
-    }
-    const qstartIndex = columnNames.indexOf('qstart');
-    if (qstartIndex === -1) {
-        throw new Error('Missing required column "qstart"');
-    }
-    const qendIndex = columnNames.indexOf('qend');
-    if (qendIndex === -1) {
-        throw new Error('Missing required column "qend"');
-    }
-    const sstartIndex = columnNames.indexOf('sstart');
-    if (sstartIndex === -1) {
-        throw new Error('Missing required column "sstart"');
-    }
-    const sendIndex = columnNames.indexOf('send');
-    if (sendIndex === -1) {
-        throw new Error('Missing required column "send"');
-    }
-    const columnNameSet = new Map(columnNames
-        .map((c, idx) => [c, idx])
-        .filter(f => !['qseqid', 'sseqid', 'qstart', 'qend', 'sstart', 'send'].includes(f[0])));
-    return (line) => {
-        if (line.startsWith('#')) {
-            return;
-        }
-        const row = line.split('\t');
-        const qseqid = row[qseqidIndex];
-        const sseqid = row[sseqidIndex];
-        const qstart = row[qstartIndex];
-        const qend = row[qendIndex];
-        const sstart = row[sstartIndex];
-        const send = row[sendIndex];
-        if (!(qseqid && sseqid && qstart && qend && sstart && send)) {
-            console.warn('Invalid BLAST line');
-            console.warn(line);
-            return;
-        }
-        const record = {
-            qseqid,
-            sseqid,
-            qstart: Number.parseInt(qstart),
-            qend: Number.parseInt(qend),
-            sstart: Number.parseInt(sstart),
-            send: Number.parseInt(send),
-        };
-        for (const [columnName, idx] of columnNameSet.entries()) {
-            const value = row[idx];
-            if (!value) {
-                continue;
-            }
-            record[columnName] = value;
-        }
-        return record;
-    };
-}
-class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    getData(opts) {
-        if (!this.data) {
-            this.data = this.setup(opts).catch((e) => {
-                this.data = undefined;
-                throw e;
-            });
-        }
-        return this.data;
-    }
-    async setup(opts) {
-        const columns = (0, configuration_1.readConfObject)(this.config, 'columns');
-        const lines = [];
-        const cb = createBlastLineParser(columns);
-        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'blastTableLocation'), this.pluginManager), opts), line => {
-            const res = cb(line);
-            if (res) {
-                lines.push(res);
-            }
-            return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        return lines;
-    }
-    async hasDataForRefName() {
-        return true;
-    }
-    getAssemblyNames() {
-        const assemblyNames = this.getConf('assemblyNames');
-        if (assemblyNames.length === 0) {
-            const query = this.getConf('queryAssembly');
-            const target = this.getConf('targetAssembly');
-            return [query, target];
-        }
-        return assemblyNames;
-    }
-    async getRefNames(opts = {}) {
-        var _a;
-        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);
-        if (idx !== -1) {
-            const set = new Set();
-            for (const feat of feats) {
-                set.add(idx === 0 ? feat.qseqid : feat.sseqid);
-            }
-            return [...set];
-        }
-        console.warn('Unable to do ref renaming on adapter');
-        return [];
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const blastRecords = await this.getData(opts);
-            const [queryAssembly, targetAssembly] = this.getAssemblyNames();
-            const { refName: queryRefName, assemblyName: queryAssemblyName, start: queryStart, end: queryEnd, } = query;
-            if (queryAssemblyName !== targetAssembly &&
-                queryAssemblyName !== queryAssembly) {
-                console.warn(`${queryAssemblyName} not found in this adapter`);
-                observer.complete();
-                return;
-            }
-            for (let i = 0; i < blastRecords.length; i++) {
-                const r = blastRecords[i];
-                let start;
-                let end;
-                let refName;
-                let assemblyName;
-                let mateStart;
-                let mateEnd;
-                let mateRefName;
-                let mateAssemblyName;
-                const { qseqid, sseqid, qstart, qend, sstart, send, ...rest } = r;
-                if (queryAssemblyName === queryAssembly) {
-                    start = qstart;
-                    end = qend;
-                    refName = qseqid;
-                    assemblyName = queryAssembly;
-                    mateStart = sstart;
-                    mateEnd = send;
-                    mateRefName = sseqid;
-                    mateAssemblyName = targetAssembly;
-                }
-                else {
-                    start = sstart;
-                    end = send;
-                    refName = sseqid;
-                    assemblyName = targetAssembly;
-                    mateStart = qstart;
-                    mateEnd = qend;
-                    mateRefName = qseqid;
-                    mateAssemblyName = queryAssembly;
-                }
-                let strand = 1;
-                let mateStrand = 1;
-                if (start > end) {
-                    ;
-                    [start, end] = [end, start];
-                    strand = -1;
-                }
-                if (mateStart > mateEnd) {
-                    ;
-                    [mateStart, mateEnd] = [mateEnd, mateStart];
-                    mateStrand = -1;
-                }
-                if (refName === queryRefName &&
-                    (0, util_1.doesIntersect2)(queryStart, queryEnd, start, end)) {
-                    observer.next(new SyntenyFeature_1.default({
-                        uniqueId: i + queryAssemblyName,
-                        assemblyName,
-                        start,
-                        end,
-                        type: 'match',
-                        refName,
-                        strand: strand * mateStrand,
-                        syntenyId: i,
-                        ...rest,
-                        mate: {
-                            start: mateStart,
-                            end: mateEnd,
-                            refName: mateRefName,
-                            assemblyName: mateAssemblyName,
-                        },
-                    }));
-                }
-            }
-            observer.complete();
-        });
-    }
-}
-BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = BlastTabularAdapter;

package/dist/BlastTabularAdapter/configSchema.d.ts

@@ -1,30 +0,0 @@
-declare const BlastTabularAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-    targetAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    queryAssembly: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    blastTableLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    columns: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BlastTabularAdapter;