@jbrowse/plugin-comparative-adapters 3.6.5 → 4.0.0

package/esm/BlastTabularAdapter/BlastTabularAdapter.js

@@ -4,7 +4,7 @@ import { doesIntersect2, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SyntenyFeature from '../SyntenyFeature';
+import SyntenyFeature from "../SyntenyFeature/index.js";
 function createBlastLineParser(columns) {
     const columnNames = columns.trim().split(' ');
     const qseqidIndex = columnNames.indexOf('qseqid');
@@ -68,7 +68,9 @@ function createBlastLineParser(columns) {
         return record;
     };
 }
-class BlastTabularAdapter extends BaseFeatureDataAdapter {
+export default class BlastTabularAdapter extends BaseFeatureDataAdapter {
+    data;
+    static capabilities = ['getFeatures', 'getRefNames'];
     getData(opts) {
         if (!this.data) {
             this.data = this.setup(opts).catch((e) => {
@@ -88,7 +90,7 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
                 lines.push(res);
             }
             return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        }, opts?.statusCallback);
         return lines;
     }
     async hasDataForRefName() {
@@ -104,8 +106,7 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
         return assemblyNames;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const r1 = opts.regions?.[0].assemblyName;
         const feats = await this.getData(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
         if (idx !== -1) {
@@ -172,6 +173,8 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
                     [mateStart, mateEnd] = [mateEnd, mateStart];
                     mateStrand = -1;
                 }
+                start -= 1;
+                mateStart -= 1;
                 if (refName === queryRefName &&
                     doesIntersect2(queryStart, queryEnd, start, end)) {
                     observer.next(new SyntenyFeature({
@@ -197,5 +200,3 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
         });
     }
 }
-BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default BlastTabularAdapter;

package/esm/BlastTabularAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BlastTabularAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BlastTabularAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -26,5 +26,5 @@ declare const BlastTabularAdapter: import("@jbrowse/core/configuration/configura
         description: string;
         defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BlastTabularAdapter;

package/esm/BlastTabularAdapter/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 BlastTabularAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'BlastTabularAdapter',
@@ -8,6 +8,6 @@ export default function BlastTabularAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./BlastTabularAdapter').then(r => r.default),
+        getAdapterClass: () => import("./BlastTabularAdapter.js").then(r => r.default),
     }));
 }

package/esm/ChainAdapter/ChainAdapter.d.ts

@@ -1,19 +1,5 @@
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class ChainAdapter extends PAFAdapter {
-    setupPre(opts?: BaseOptions): Promise<{
-        qname: string;
-        qstart: number;
-        qend: number;
-        tname: string;
-        tstart: number;
-        tend: number;
-        strand: number;
-        extra: {
-            numMatches: number;
-            blockLen: number;
-            mappingQual: number;
-            cg: string;
-        };
-    }[]>;
+    setupPre(opts?: BaseOptions): Promise<import("../PAFAdapter/util.ts").PAFRecord[]>;
 }

package/esm/ChainAdapter/ChainAdapter.js

@@ -1,9 +1,10 @@
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { paf_chain2paf } from './util';
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { paf_chain2paf } from "./util.js";
+import PAFAdapter from "../PAFAdapter/PAFAdapter.js";
+import { getWeightedMeans } from "../PAFAdapter/util.js";
 export default class ChainAdapter extends PAFAdapter {
     async setupPre(opts) {
-        return paf_chain2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('chainLocation'), this.pluginManager), opts), opts);
+        return getWeightedMeans(paf_chain2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('chainLocation'), this.pluginManager), opts), opts));
     }
 }

package/esm/ChainAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const ChainAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const ChainAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -21,5 +21,5 @@ declare const ChainAdapter: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default ChainAdapter;

package/esm/ChainAdapter/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 ChainAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ChainAdapter',
@@ -8,6 +8,6 @@ export default function ChainAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./ChainAdapter').then(r => r.default),
+        getAdapterClass: () => import("./ChainAdapter.js").then(r => r.default),
     }));
 }

package/esm/ChainAdapter/util.js

@@ -59,7 +59,7 @@ export function paf_chain2paf(buffer, opts) {
             const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
             if (size_ungapped_alignment !== 0) {
-                num_matches += +size_ungapped_alignment;
+                num_matches += size_ungapped_alignment;
                 cigar += `${size_ungapped_alignment}M`;
             }
             if (diff_in_query !== 0) {
@@ -70,9 +70,9 @@ export function paf_chain2paf(buffer, opts) {
             }
         }
         return true;
-    }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+    }, opts?.statusCallback);
     if (cigar) {
-        generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
+        records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
     }
     statusCallback('');
     return records;

package/esm/ComparativeAddTrackComponent/ComparativeAddTrackComponent.js

@@ -3,11 +3,10 @@ import { useEffect, useState } from 'react';
 import { AssemblySelector } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-const ComparativeAddTrackComponent = observer(function ({ model }) {
-    var _a, _b;
+const ComparativeAddTrackComponent = observer(function ComparativeAddTrackComponent({ model }) {
     const session = getSession(model);
-    const [r0, setR0] = useState((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
-    const [r1, setR1] = useState((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
+    const [r0, setR0] = useState(session.assemblies[0]?.name);
+    const [r1, setR1] = useState(session.assemblies[0]?.name);
     useEffect(() => {
         model.setMixinData({
             adapter: {

package/esm/ComparativeAddTrackComponent/index.js

@@ -1,6 +1,6 @@
 import { lazy } from 'react';
-import { pairwiseTypes } from '../syntenyTypes';
-const ComparativeAddTrackComponent = lazy(() => import('./ComparativeAddTrackComponent'));
+import { pairwiseTypes } from "../syntenyTypes.js";
+const ComparativeAddTrackComponent = lazy(() => import("./ComparativeAddTrackComponent.js"));
 export default function ComparativeAddTrackComponentF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
         return pairwiseTypes.includes(model.trackAdapterType)

package/esm/DeltaAdapter/DeltaAdapter.d.ts

@@ -1,14 +1,5 @@
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class DeltaAdapter extends PAFAdapter {
-    setupPre(opts?: BaseOptions): Promise<{
-        qname: string;
-        qstart: number;
-        qend: number;
-        tname: string;
-        tstart: number;
-        tend: number;
-        strand: number;
-        extra: Record<string, unknown>;
-    }[]>;
+    setupPre(opts?: BaseOptions): Promise<import("../PAFAdapter/util.ts").PAFRecord[]>;
 }

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -1,9 +1,10 @@
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { paf_delta2paf } from './util';
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { paf_delta2paf } from "./util.js";
+import PAFAdapter from "../PAFAdapter/PAFAdapter.js";
+import { getWeightedMeans } from "../PAFAdapter/util.js";
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
-        return paf_delta2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('deltaLocation'), this.pluginManager), opts), opts);
+        return getWeightedMeans(paf_delta2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('deltaLocation'), this.pluginManager), opts), opts));
     }
 }

package/esm/DeltaAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const DeltaAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -21,5 +21,5 @@ declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default DeltaAdapter;

package/esm/DeltaAdapter/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 DeltaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'DeltaAdapter',
@@ -8,6 +8,6 @@ export default function DeltaAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./DeltaAdapter').then(r => r.default),
+        getAdapterClass: () => import("./DeltaAdapter.js").then(r => r.default),
     }));
 }

package/esm/DeltaAdapter/util.js

@@ -14,7 +14,7 @@ export function paf_delta2paf(buffer, opts) {
     let y = 0;
     let seen_gt = false;
     const records = [];
-    const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
+    const regex = /^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/;
     parseLineByLine(buffer, line => {
         const m = regex.exec(line);
         if (m !== null) {
@@ -34,10 +34,10 @@ export function paf_delta2paf(buffer, opts) {
             const t3 = +t[3];
             const t4 = +t[4];
             strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
-            rs = +Math.min(t0, t1) - 1;
-            re = +Math.max(t1, t0);
-            qs = +Math.min(t2, t3) - 1;
-            qe = +Math.max(t3, t2);
+            rs = Math.min(t0, t1) - 1;
+            re = Math.max(t1, t0);
+            qs = Math.min(t2, t3) - 1;
+            qe = Math.max(t3, t2);
             x = y = 0;
             NM = t4;
             cigar = [];

package/esm/GuessAdapter/index.js

@@ -1,6 +1,6 @@
 import { testAdapter } from '@jbrowse/core/util';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
-import { syntenyTypes } from '../syntenyTypes';
+import { syntenyTypes } from "../syntenyTypes.js";
 export default function GuessAdapterF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {

package/esm/MCScanAddTrackComponent/MCScanAddTrackComponent.d.ts

@@ -1,2 +1,2 @@
-declare const MCScanAddTrackComponent: ({ model }: any) => import("react/jsx-runtime").JSX.Element;
+declare const MCScanAddTrackComponent: ({ model, }: any) => import("react/jsx-runtime").JSX.Element;
 export default MCScanAddTrackComponent;

package/esm/MCScanAddTrackComponent/MCScanAddTrackComponent.js

@@ -4,11 +4,10 @@ import { AssemblySelector, FileSelector } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-const MCScanAddTrackComponent = observer(function ({ model }) {
-    var _a, _b;
+const MCScanAddTrackComponent = observer(function MCScanAddTrackComponent({ model, }) {
     const session = getSession(model);
-    const [r0, setR0] = useState((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
-    const [r1, setR1] = useState((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
+    const [r0, setR0] = useState(session.assemblies[0]?.name);
+    const [r1, setR1] = useState(session.assemblies[0]?.name);
     const [bed1Location, setBed1Location] = useState();
     const [bed2Location, setBed2Location] = useState();
     useEffect(() => {

package/esm/MCScanAddTrackComponent/index.js

@@ -1,6 +1,6 @@
 import { lazy } from 'react';
-import { mcscanTypes } from '../syntenyTypes';
-const MCScanAddTrackComponent = lazy(() => import('./MCScanAddTrackComponent'));
+import { mcscanTypes } from "../syntenyTypes.js";
+const MCScanAddTrackComponent = lazy(() => import("./MCScanAddTrackComponent.js"));
 export default function MCScanAddTrackComponentF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
         return mcscanTypes.includes(model.trackAdapterType)

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -2,8 +2,10 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { SimpleFeature, doesIntersect2, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { parseBed, readFile } from '../util';
-class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+import { parseBed, readFile } from "../util.js";
+export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    static capabilities = ['getFeatures', 'getRefNames'];
     async setup(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
@@ -48,8 +50,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         return assemblyNames;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const r1 = opts.regions?.[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
         if (idx !== -1) {
@@ -92,5 +93,3 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         });
     }
 }
-MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default MCScanAnchorsAdapter;

package/esm/MCScanAnchorsAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const MCScanAnchorsAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     mcscanAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -24,5 +24,5 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
         type: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default MCScanAnchorsAdapter;

package/esm/MCScanAnchorsAdapter/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 MCScanAnchorsAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'MCScanAnchorsAdapter',
@@ -8,6 +8,6 @@ export default function MCScanAnchorsAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./MCScanAnchorsAdapter').then(r => r.default),
+        getAdapterClass: () => import("./MCScanAnchorsAdapter.js").then(r => r.default),
     }));
 }

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -3,8 +3,10 @@ import { doesIntersect2, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { parseBed, readFile } from '../util';
-class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+import { parseBed, readFile } from "../util.js";
+export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    static capabilities = ['getFeatures', 'getRefNames'];
     async setup(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
@@ -59,8 +61,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         return assemblyNames;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const r1 = opts.regions?.[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
         if (idx !== -1) {
@@ -123,5 +124,3 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         });
     }
 }
-MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default MCScanAnchorsAdapter;

package/esm/MCScanSimpleAnchorsAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const MCScanSimpleAnchorsAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     mcscanSimpleAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -24,5 +24,5 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
         type: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default MCScanSimpleAnchorsAdapter;

package/esm/MCScanSimpleAnchorsAdapter/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 MCScanSimpleAnchorsAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'MCScanSimpleAnchorsAdapter',
@@ -8,6 +8,6 @@ export default function MCScanSimpleAnchorsAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./MCScanSimpleAnchorsAdapter').then(r => r.default),
+        getAdapterClass: () => import("./MCScanSimpleAnchorsAdapter.js").then(r => r.default),
     }));
 }

package/esm/MashMapAdapter/MashMapAdapter.d.ts

@@ -1,16 +1,5 @@
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class MashMapAdapter extends PAFAdapter {
-    setupPre(opts?: BaseOptions): Promise<{
-        tname: string;
-        tstart: number;
-        tend: number;
-        qname: string;
-        qstart: number;
-        qend: number;
-        strand: number;
-        extra: {
-            mappingQual: number;
-        };
-    }[]>;
+    setupPre(opts?: BaseOptions): Promise<import("../PAFAdapter/util.ts").PAFRecord[]>;
 }

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,15 +1,16 @@
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import PAFAdapter from "../PAFAdapter/PAFAdapter.js";
+import { getWeightedMeans } from "../PAFAdapter/util.js";
 export default class MashMapAdapter extends PAFAdapter {
     async setupPre(opts) {
         const lines = [];
         parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('outLocation'), this.pluginManager), opts), line => {
             lines.push(parseMashMapLine(line));
             return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        return lines;
+        }, opts?.statusCallback);
+        return getWeightedMeans(lines);
     }
 }
 function parseMashMapLine(line) {

package/esm/MashMapAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const MashMapAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const MashMapAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -21,5 +21,5 @@ declare const MashMapAdapter: import("@jbrowse/core/configuration/configurationS
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default MashMapAdapter;

package/esm/MashMapAdapter/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 MashMapAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'MashMapAdapter',
@@ -8,6 +8,6 @@ export default function MashMapAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
+        getAdapterClass: () => import("./MashMapAdapter.js").then(r => r.default),
     }));
 }

package/esm/PAFAdapter/PAFAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { PAFRecord } from './util';
+import type { PAFRecord } from './util.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';

package/esm/PAFAdapter/PAFAdapter.js

@@ -1,4 +1,3 @@
-import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -6,11 +5,13 @@ import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-import SyntenyFeature from '../SyntenyFeature';
-import { flipCigar, parsePAFLine, swapIndelCigar } from '../util';
-import { getWeightedMeans } from './util';
+import SyntenyFeature from "../SyntenyFeature/index.js";
+import { flipCigar, parsePAFLine, swapIndelCigar } from "../util.js";
+import { getWeightedMeans } from "./util.js";
 const { parseCigar } = MismatchParser;
-class PAFAdapter extends BaseFeatureDataAdapter {
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    static capabilities = ['getFeatures', 'getRefNames'];
     async setup(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
@@ -25,8 +26,8 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('pafLocation'), this.pluginManager), opts), line => {
             lines.push(parsePAFLine(line));
             return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        return lines;
+        }, opts?.statusCallback);
+        return getWeightedMeans(lines);
     }
     async hasDataForRefName() {
         return true;
@@ -41,8 +42,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return assemblyNames;
     }
     async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const r1 = opts.regions?.[0].assemblyName;
         const feats = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
         if (idx !== -1) {
@@ -57,11 +57,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
-            let pafRecords = await this.setup(opts);
-            const { config } = opts;
-            if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
-                pafRecords = getWeightedMeans(pafRecords);
-            }
+            const pafRecords = await this.setup(opts);
             const assemblyNames = this.getAssemblyNames();
             const { start: qstart, end: qend, refName: qref, assemblyName } = query;
             const index = assemblyNames.indexOf(assemblyName);
@@ -133,5 +129,3 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         });
     }
 }
-PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default PAFAdapter;

package/esm/PAFAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const PAFAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     assemblyNames: {
         type: string;
         defaultValue: never[];
@@ -21,5 +21,5 @@ declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PAFAdapter;

package/esm/PAFAdapter/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 PAFAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'PAFAdapter',
@@ -8,6 +8,6 @@ export default function PAFAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Synteny adapters',
         },
-        getAdapterClass: () => import('./PAFAdapter').then(r => r.default),
+        getAdapterClass: () => import("./PAFAdapter.js").then(r => r.default),
     }));
 }