@jbrowse/plugin-comparative-adapters 2.16.1 → 2.18.0

package/dist/PAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pafLocation: {
         type: string;
         defaultValue: {

package/dist/PAFAdapter/configSchema.js

@@ -1,38 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config PAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PAFAdapter = (0, configuration_1.ConfigurationSchema)('PAFAdapter', {
-    /**
-     * #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
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pafLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/PAFAdapter/index.d.ts

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

package/dist/PAFAdapter/util.d.ts

@@ -9,7 +9,7 @@ export interface PAFRecord {
     extra: {
         cg?: string;
         blockLen?: number;
-        mappingQual: number;
+        mappingQual?: number;
         numMatches?: number;
         meanScore?: number;
     };

package/dist/PAFAdapter/util.js

@@ -2,40 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getWeightedMeans = getWeightedMeans;
 const util_1 = require("../util");
-// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
-// License reproduced here
-//
-// MIT License
-// Copyright (c) 2017 Tom Poorten
-// 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.
-//
-// Notes: in the weighted mean longer alignments factor in more heavily of all
-// the fragments of a query vs the reference that it mapped to
-//
-// this uses a combined key query+'-'+ref to iteratively map all the alignments
-// that match a particular ref from a particular query (so 1d array of what
-// could be a 2d map)
-//
-// the result is a single number that says e.g. chr5 from human mapped to chr5
-// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
-// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
-// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
-// this can show strong and weak levels of synteny, especially in polyploidy
-// situations
 function getWeightedMeans(ret) {
     const scoreMap = {};
     for (const entry of ret) {
@@ -45,7 +11,7 @@ function getWeightedMeans(ret) {
         if (!scoreMap[key]) {
             scoreMap[key] = { quals: [], len: [] };
         }
-        scoreMap[key].quals.push(entry.extra.mappingQual);
+        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]) => {
@@ -70,7 +36,6 @@ function getWeightedMeans(ret) {
     }
     return ret;
 }
-// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import PluginManager from '@jbrowse/core/PluginManager';
 import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -3,13 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const tabix_1 = require("@gmod/tabix");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const io_1 = require("@jbrowse/core/util/io");
-const tabix_1 = require("@gmod/tabix");
-// locals
-const util_1 = require("../util");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
+const util_1 = require("../util");
 class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -98,12 +97,12 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                         },
                     }));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = PAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: string;
         description: string;
@@ -34,21 +22,12 @@ declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/con
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {

package/dist/PairwiseIndexedPAFAdapter/configSchema.js

@@ -2,38 +2,23 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config PairwiseIndexedPAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PairwiseIndexedPAFAdapter = (0, configuration_1.ConfigurationSchema)('PairwiseIndexedPAFAdapter', {
-    /**
-     * #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
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: 'fileLocation',
         description: 'location of pairwise tabix indexed PAF (pif)',
@@ -42,21 +27,12 @@ const PairwiseIndexedPAFAdapter = (0, configuration_1.ConfigurationSchema)('Pair
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {

package/dist/PairwiseIndexedPAFAdapter/index.d.ts

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

package/dist/SyntenyFeature/index.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-// locals
 const { getMismatches } = plugin_alignments_1.MismatchParser;
 class SyntenyFeature extends util_1.SimpleFeature {
     get(arg) {

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class ComparativeAdaptersPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,14 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const PAFAdapter_1 = __importDefault(require("./PAFAdapter"));
-const PairwiseIndexedPAFAdapter_1 = __importDefault(require("./PairwiseIndexedPAFAdapter"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const BlastTabularAdapter_1 = __importDefault(require("./BlastTabularAdapter"));
+const ChainAdapter_1 = __importDefault(require("./ChainAdapter"));
+const DeltaAdapter_1 = __importDefault(require("./DeltaAdapter"));
 const MCScanAnchorsAdapter_1 = __importDefault(require("./MCScanAnchorsAdapter"));
 const MCScanSimpleAnchorsAdapter_1 = __importDefault(require("./MCScanSimpleAnchorsAdapter"));
 const MashMapAdapter_1 = __importDefault(require("./MashMapAdapter"));
-const DeltaAdapter_1 = __importDefault(require("./DeltaAdapter"));
-const ChainAdapter_1 = __importDefault(require("./ChainAdapter"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const PAFAdapter_1 = __importDefault(require("./PAFAdapter"));
+const PairwiseIndexedPAFAdapter_1 = __importDefault(require("./PairwiseIndexedPAFAdapter"));
 class ComparativeAdaptersPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -25,6 +26,7 @@ class ComparativeAdaptersPlugin extends Plugin_1.default {
         (0, MCScanAnchorsAdapter_1.default)(pluginManager);
         (0, MCScanSimpleAnchorsAdapter_1.default)(pluginManager);
         (0, MashMapAdapter_1.default)(pluginManager);
+        (0, BlastTabularAdapter_1.default)(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.paf/i;

package/dist/util.d.ts

@@ -1,7 +1,7 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { GenericFilehandle } from 'generic-filehandle';
+import type { PAFRecord } from './PAFAdapter/util';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Buffer } from 'buffer';
-import { PAFRecord } from './PAFAdapter/util';
+import type { GenericFilehandle } from 'generic-filehandle';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;
     start: number;
@@ -12,7 +12,7 @@ export declare function parseBed(text: string): Map<string | undefined, {
 }>;
 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 parseLineByLine<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -7,7 +7,6 @@ exports.parseLineByLine = parseLineByLine;
 exports.parsePAFLine = parsePAFLine;
 exports.flipCigar = flipCigar;
 exports.swapIndelCigar = swapIndelCigar;
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("@jbrowse/core/util");
 function parseBed(text) {
     return new Map(text
@@ -29,25 +28,29 @@ function parseBed(text) {
     }));
 }
 async function readFile(file, opts) {
-    const buffer = (await file.readFile(opts));
-    return new TextDecoder('utf8', { fatal: true }).decode((0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer);
+    const buf = await (0, util_1.fetchAndMaybeUnzip)(file, opts);
+    const decoder = new TextDecoder('utf8');
+    return decoder.decode(buf);
 }
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function parseLineByLine(buffer, cb) {
     let blockStart = 0;
     const entries = [];
+    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();
         if (line) {
-            entries.push(cb(line));
+            const entry = cb(line);
+            if (entry) {
+                entries.push(entry);
+            }
         }
         blockStart = n + 1;
     }

package/esm/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -0,0 +1,66 @@
+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>;
+    freeResources(): void;
+}
+export {};