@jbrowse/plugin-comparative-adapters 2.6.1

package/esm/PAFAdapter/PAFAdapter.js

@@ -0,0 +1,147 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { unzip } from '@gmod/bgzf-filehandle';
+import { MismatchParser } from '@jbrowse/plugin-alignments';
+// locals
+import SyntenyFeature from './SyntenyFeature';
+import { isGzip, parseLineByLine } from '../util';
+import { getWeightedMeans, flipCigar, swapIndelCigar, parsePAFLine, } from './util';
+const { parseCigar } = MismatchParser;
+class PAFAdapter extends BaseFeatureDataAdapter {
+    async setup(opts) {
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async setupPre(opts) {
+        const pm = this.pluginManager;
+        const pafLocation = openLocation(this.getConf('pafLocation'), pm);
+        const buffer = (await pafLocation.readFile(opts));
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        return parseLineByLine(buf, parsePAFLine);
+    }
+    async hasDataForRefName() {
+        // determining this properly is basically a call to getFeatures
+        // so is not really that important, and has to be true or else
+        // getFeatures is never called (BaseAdapter filters it out)
+        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;
+        // @ts-expect-error
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const feats = await this.setup(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                set.add(idx === 0 ? feat.qname : feat.tname);
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            let pafRecords = await this.setup(opts);
+            const { config } = opts;
+            // note: this is not the adapter config, it is responding to a display
+            // setting passed in via the opts parameter
+            if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
+                pafRecords = getWeightedMeans(pafRecords);
+            }
+            const assemblyNames = this.getAssemblyNames();
+            // The index of the assembly name in the query list corresponds to the
+            // adapter in the subadapters list
+            const index = assemblyNames.indexOf(query.assemblyName);
+            const { start: qstart, end: qend, refName: qref, assemblyName } = query;
+            if (index === -1) {
+                console.warn(`${assemblyName} not found in this adapter`);
+                observer.complete();
+            }
+            for (let i = 0; i < pafRecords.length; i++) {
+                const r = pafRecords[i];
+                let start = 0;
+                let end = 0;
+                let refName = '';
+                let mateName = '';
+                let mateStart = 0;
+                let mateEnd = 0;
+                const flip = index === 0;
+                const assemblyName = assemblyNames[+!flip];
+                if (index === 0) {
+                    start = r.qstart;
+                    end = r.qend;
+                    refName = r.qname;
+                    mateName = r.tname;
+                    mateStart = r.tstart;
+                    mateEnd = r.tend;
+                }
+                else {
+                    start = r.tstart;
+                    end = r.tend;
+                    refName = r.tname;
+                    mateName = r.qname;
+                    mateStart = r.qstart;
+                    mateEnd = r.qend;
+                }
+                const { extra, strand } = r;
+                if (refName === qref && doesIntersect2(qstart, qend, start, end)) {
+                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
+                    let CIGAR = extra.cg;
+                    if (extra.cg) {
+                        if (flip && strand === -1) {
+                            CIGAR = flipCigar(parseCigar(extra.cg)).join('');
+                        }
+                        else if (flip) {
+                            CIGAR = swapIndelCigar(extra.cg);
+                        }
+                    }
+                    observer.next(new SyntenyFeature({
+                        uniqueId: i + assemblyName,
+                        assemblyName,
+                        start,
+                        end,
+                        type: 'match',
+                        refName,
+                        strand,
+                        ...rest,
+                        CIGAR,
+                        syntenyId: i,
+                        identity: numMatches / blockLen,
+                        numMatches,
+                        blockLen,
+                        mate: {
+                            start: mateStart,
+                            end: mateEnd,
+                            refName: mateName,
+                            assemblyName: assemblyNames[+flip],
+                        },
+                    }));
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources( /* { query } */) { }
+}
+PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default PAFAdapter;
+//# sourceMappingURL=PAFAdapter.js.map

package/esm/PAFAdapter/PAFAdapter.js.map

@@ -0,0 +1 @@
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package/esm/PAFAdapter/SyntenyFeature.d.ts

@@ -0,0 +1,4 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+export default class SyntenyFeature extends SimpleFeature {
+    get(arg: string): any;
+}

package/esm/PAFAdapter/SyntenyFeature.js

@@ -0,0 +1,14 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+import { MismatchParser } from '@jbrowse/plugin-alignments';
+// locals
+const { getMismatches } = MismatchParser;
+export default class SyntenyFeature extends SimpleFeature {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    get(arg) {
+        if (arg === 'mismatches') {
+            return getMismatches(this.get('CIGAR'));
+        }
+        return super.get(arg);
+    }
+}
+//# sourceMappingURL=SyntenyFeature.js.map

package/esm/PAFAdapter/SyntenyFeature.js.map

@@ -0,0 +1 @@
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package/esm/PAFAdapter/configSchema.d.ts

@@ -0,0 +1,37 @@
+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: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PAFAdapter;

package/esm/PAFAdapter/configSchema.js

@@ -0,0 +1,43 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config PAFAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const PAFAdapter = ConfigurationSchema('PAFAdapter', {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query 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: {
+            uri: '/path/to/file.paf',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+export default PAFAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/PAFAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/PAFAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/PAFAdapter/index.js

@@ -0,0 +1,14 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'PAFAdapter',
+        displayName: 'PAF adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./PAFAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/PAFAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/PAFAdapter/util.d.ts

@@ -0,0 +1,20 @@
+export interface PAFRecord {
+    qname: string;
+    qstart: number;
+    qend: number;
+    tname: string;
+    tstart: number;
+    tend: number;
+    strand: number;
+    extra: {
+        cg?: string;
+        blockLen?: number;
+        mappingQual: number;
+        numMatches?: number;
+        meanScore?: number;
+    };
+}
+export declare function getWeightedMeans(ret: PAFRecord[]): PAFRecord[];
+export declare function parsePAFLine(line: string): PAFRecord;
+export declare function flipCigar(cigar: string[]): string[];
+export declare function swapIndelCigar(cigar: string): string;

package/esm/PAFAdapter/util.js

@@ -0,0 +1,127 @@
+import { zip } from '../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
+export function getWeightedMeans(ret) {
+    const scoreMap = {};
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const query = entry.qname;
+        const target = entry.tname;
+        const key = query + '-' + target;
+        if (!scoreMap[key]) {
+            scoreMap[key] = { quals: [], len: [] };
+        }
+        scoreMap[key].quals.push(entry.extra.mappingQual);
+        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 (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const query = entry.qname;
+        const target = entry.tname;
+        const key = query + '-' + target;
+        entry.extra.meanScore = meanScoreMap[key];
+    }
+    let min = 10000;
+    let max = 0;
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        min = Math.min(entry.extra.meanScore || 0, min);
+        max = Math.max(entry.extra.meanScore || 0, max);
+    }
+    for (let i = 0; i < ret.length; i++) {
+        const entry = ret[i];
+        const b = entry.extra.meanScore || 0;
+        entry.extra.meanScore = (b - min) / (max - min);
+    }
+    return ret;
+}
+// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
+function weightedMean(tuples) {
+    // eslint-disable-next-line unicorn/no-array-reduce
+    const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
+        valueSum + value * weight,
+        weightSum + weight,
+    ], [0, 0]);
+    return valueSum / weightSum;
+}
+export function parsePAFLine(line) {
+    const [qname, , qstart, qend, strand, tname, , tstart, tend, numMatches, blockLen, mappingQual, ...fields] = line.split('\t');
+    const rest = Object.fromEntries(fields.map(field => {
+        const r = field.indexOf(':');
+        const fieldName = field.slice(0, r);
+        const fieldValue = field.slice(r + 3);
+        return [fieldName, fieldValue];
+    }));
+    return {
+        tname,
+        tstart: +tstart,
+        tend: +tend,
+        qname,
+        qstart: +qstart,
+        qend: +qend,
+        strand: strand === '-' ? -1 : 1,
+        extra: {
+            numMatches: +numMatches,
+            blockLen: +blockLen,
+            mappingQual: +mappingQual,
+            ...rest,
+        },
+    };
+}
+export function flipCigar(cigar) {
+    const arr = [];
+    for (let i = cigar.length - 2; i >= 0; i -= 2) {
+        arr.push(cigar[i]);
+        const op = cigar[i + 1];
+        if (op === 'D') {
+            arr.push('I');
+        }
+        else if (op === 'I') {
+            arr.push('D');
+        }
+        else {
+            arr.push(op);
+        }
+    }
+    return arr;
+}
+export function swapIndelCigar(cigar) {
+    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
+}
+//# sourceMappingURL=util.js.map

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package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class ComparativeAdaptersPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,45 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PAFAdapterF from './PAFAdapter';
+import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
+import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
+import MashMapAdapterF from './MashMapAdapter';
+import DeltaAdapterF from './DeltaAdapter';
+import ChainAdapterF from './ChainAdapter';
+import { getFileName, } from '@jbrowse/core/util/tracks';
+export default class ComparativeAdaptersPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'ComparativeAdaptersPlugin';
+    }
+    install(pluginManager) {
+        PAFAdapterF(pluginManager);
+        DeltaAdapterF(pluginManager);
+        ChainAdapterF(pluginManager);
+        MCScanAnchorsAdapterF(pluginManager);
+        MCScanSimpleAnchorsAdapterF(pluginManager);
+        MashMapAdapterF(pluginManager);
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.paf/i;
+                const adapterName = 'PAFAdapter';
+                const fileName = getFileName(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        pafLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'PAFAdapter') {
+                    return 'SyntenyTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/esm/util.d.ts

@@ -0,0 +1,16 @@
+/// <reference types="node" />
+import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { GenericFilehandle } from 'generic-filehandle';
+import { PAFRecord } from './PAFAdapter/util';
+export declare function isGzip(buf: Buffer): boolean;
+export declare function parseBed(text: string): Map<string, {
+    refName: string;
+    start: number;
+    end: number;
+    score: number;
+    name: string;
+    strand: number;
+}>;
+export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
+export declare function zip(a: number[], b: number[]): [number, number][];
+export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];

package/esm/util.js

@@ -0,0 +1,49 @@
+import { unzip } from '@gmod/bgzf-filehandle';
+export function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export function parseBed(text) {
+    return new Map(text
+        .split(/\n|\r\n|\r/)
+        .filter(f => !!f || f.startsWith('#'))
+        .map(line => {
+        const [refName, start, end, name, score, strand] = line.split('\t');
+        return [
+            name,
+            {
+                refName,
+                start: +start,
+                end: +end,
+                score: +score,
+                name,
+                strand: strand === '-' ? -1 : 1,
+            },
+        ];
+    }));
+}
+export async function readFile(file, opts) {
+    const buffer = (await file.readFile(opts));
+    return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await unzip(buffer) : buffer);
+}
+export function zip(a, b) {
+    return a.map((e, i) => [e, b[i]]);
+}
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+export function parseLineByLine(buffer, cb) {
+    let blockStart = 0;
+    const entries = [];
+    while (blockStart < buffer.length) {
+        const n = buffer.indexOf('\n', blockStart);
+        if (n === -1) {
+            break;
+        }
+        const b = buffer.slice(blockStart, n);
+        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        if (line) {
+            entries.push(cb(line));
+        }
+        blockStart = n + 1;
+    }
+    return entries;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,63 @@
+{
+  "name": "@jbrowse/plugin-comparative-adapters",
+  "version": "2.6.1",
+  "description": "JBrowse 2 comparative adapters",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/comparative-adapters"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "dist/index.js",
+  "files": [
+    "dist",
+    "src",
+    "esm"
+  ],
+  "scripts": {
+    "build": "npm-run-all build:*",
+    "test": "cd ../..; jest 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:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
+  },
+  "dependencies": {
+    "@gmod/bgzf-filehandle": "^1.4.3",
+    "generic-filehandle": "^3.0.0"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-alignments": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "prop-types": "^15.0.0",
+    "react": ">=16.8.0",
+    "react-dom": ">=16.8.0",
+    "rxjs": "^7.0.0"
+  },
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}