@jbrowse/plugin-comparative-adapters 2.16.1 → 2.18.0

package/esm/BlastTabularAdapter/BlastTabularAdapter.js

@@ -0,0 +1,195 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { doesIntersect2, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SyntenyFeature from '../SyntenyFeature';
+import { parseLineByLine } from '../util';
+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 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 pm = this.pluginManager;
+        const buf = await fetchAndMaybeUnzip(openLocation(readConfObject(this.config, 'blastTableLocation'), pm), opts);
+        const columns = readConfObject(this.config, 'columns');
+        return parseLineByLine(buf, createBlastLineParser(columns));
+    }
+    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 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 &&
+                    doesIntersect2(queryStart, queryEnd, start, end)) {
+                    observer.next(new SyntenyFeature({
+                        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();
+        });
+    }
+    freeResources() { }
+}
+BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default BlastTabularAdapter;

package/esm/BlastTabularAdapter/configSchema.d.ts

@@ -0,0 +1,30 @@
+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;

package/esm/BlastTabularAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const BlastTabularAdapter = ConfigurationSchema('BlastTabularAdapter', {
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Query assembly is the first value in the array, target assembly is the second',
+    },
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the target assembly',
+    },
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the query assembly',
+    },
+    blastTableLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/blastTable.tsv',
+            locationType: 'UriLocation',
+        },
+    },
+    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',
+        defaultValue: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore',
+    },
+}, { explicitlyTyped: true });
+export default BlastTabularAdapter;

package/esm/BlastTabularAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function BlastTabularAdapterF(pluginManager: PluginManager): void;

package/esm/BlastTabularAdapter/index.js

@@ -0,0 +1,13 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function BlastTabularAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BlastTabularAdapter',
+        displayName: 'Tabular BLAST output adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./BlastTabularAdapter').then(r => r.default),
+    }));
+}

package/esm/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/esm/ChainAdapter/ChainAdapter.js

@@ -1,14 +1,11 @@
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { isGzip } from '@jbrowse/core/util';
-import { unzip } from '@gmod/bgzf-filehandle';
-// locals
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_chain2paf } from './util';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class ChainAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('chainLocation'), this.pluginManager);
-        const buffer = (await loc.readFile(opts));
-        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        const buf = await fetchAndMaybeUnzip(loc, opts);
         return paf_chain2paf(buf);
     }
 }

package/esm/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/esm/ChainAdapter/configSchema.js

@@ -1,39 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config ChainAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const ChainAdapter = 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/esm/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/esm/ChainAdapter/util.js

@@ -1,28 +1,3 @@
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
-/* 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,
@@ -53,34 +28,21 @@ export function paf_chain2paf(buffer) {
     let cigar = '';
     const records = [];
     let blockStart = 0;
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const l = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        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];
@@ -94,18 +56,10 @@ export 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;
@@ -121,7 +75,6 @@ export 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/esm/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/esm/DeltaAdapter/DeltaAdapter.js

@@ -1,14 +1,11 @@
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { unzip } from '@gmod/bgzf-filehandle';
-import { isGzip } from '@jbrowse/core/util';
-// locals
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_delta2paf } from './util';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);
-        const buffer = (await loc.readFile(opts));
-        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        const buf = await fetchAndMaybeUnzip(loc, opts);
         return paf_delta2paf(buf);
     }
 }

package/esm/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/esm/DeltaAdapter/configSchema.js

@@ -1,39 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DeltaAdapter = 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/esm/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/esm/DeltaAdapter/util.js

@@ -1,31 +1,3 @@
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
-/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
- *
- * The MIT License
- *
- * Copyright (c) 2018-     Dana-Farber Cancer Institute
- *               2017-2018 Broad Institute, Inc.
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject to
- * the following conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
 export function paf_delta2paf(buffer) {
     let rname = '';
     let qname = '';
@@ -43,13 +15,14 @@ export function paf_delta2paf(buffer) {
     const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
     let blockStart = 0;
     let i = 0;
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        const line = decoder.decode(b).trim();
         blockStart = n + 1;
         i++;
         if (line) {
@@ -122,7 +95,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 2);
-                    } // deletion
+                    }
                 }
                 else {
                     const l = -d - 1;
@@ -136,7 +109,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 1);
-                    } // insertion
+                    }
                 }
             }
         }

package/esm/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 {};