@jbrowse/plugin-comparative-adapters 2.8.0 → 2.10.0

package/dist/PAFAdapter/PAFAdapter.js

@@ -11,7 +11,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 // locals
-const SyntenyFeature_1 = __importDefault(require("./SyntenyFeature"));
+const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
 const util_1 = require("../util");
 const util_2 = require("./util");
 const { parseCigar } = plugin_alignments_1.MismatchParser;
@@ -30,7 +30,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pafLocation = (0, io_1.openLocation)(this.getConf('pafLocation'), pm);
         const buffer = (await pafLocation.readFile(opts));
         const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
-        return (0, util_1.parseLineByLine)(buf, util_2.parsePAFLine);
+        return (0, util_1.parseLineByLine)(buf, util_1.parsePAFLine);
     }
     async hasDataForRefName() {
         // determining this properly is basically a call to getFeatures
@@ -75,8 +75,11 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             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;
+            const index = assemblyNames.indexOf(assemblyName);
+            // if the getFeatures::query is on the query assembly, flip orientation
+            // of data
+            const flip = index === 0;
             if (index === -1) {
                 console.warn(`${assemblyName} not found in this adapter`);
                 observer.complete();
@@ -89,9 +92,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 let mateName = '';
                 let mateStart = 0;
                 let mateEnd = 0;
-                const flip = index === 0;
-                const assemblyName = assemblyNames[+!flip];
-                if (index === 0) {
+                if (flip) {
                     start = r.qstart;
                     end = r.qend;
                     refName = r.qname;
@@ -113,10 +114,10 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     let CIGAR = extra.cg;
                     if (extra.cg) {
                         if (flip && strand === -1) {
-                            CIGAR = (0, util_2.flipCigar)(parseCigar(extra.cg)).join('');
+                            CIGAR = (0, util_1.flipCigar)(parseCigar(extra.cg)).join('');
                         }
                         else if (flip) {
-                            CIGAR = (0, util_2.swapIndelCigar)(extra.cg);
+                            CIGAR = (0, util_1.swapIndelCigar)(extra.cg);
                         }
                     }
                     observer.next(new SyntenyFeature_1.default({

package/dist/PAFAdapter/util.d.ts

@@ -15,6 +15,3 @@ export interface PAFRecord {
     };
 }
 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/dist/PAFAdapter/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.swapIndelCigar = exports.flipCigar = exports.parsePAFLine = exports.getWeightedMeans = void 0;
+exports.getWeightedMeans = void 0;
 const util_1 = require("../util");
 // based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
 // License reproduced here
@@ -80,50 +80,3 @@ function weightedMean(tuples) {
     ], [0, 0]);
     return valueSum / weightSum;
 }
-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,
-        },
-    };
-}
-exports.parsePAFLine = parsePAFLine;
-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;
-}
-exports.flipCigar = flipCigar;
-function swapIndelCigar(cigar) {
-    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
-}
-exports.swapIndelCigar = swapIndelCigar;

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -0,0 +1,24 @@
+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';
+interface PAFOptions extends BaseOptions {
+    config?: AnyConfigurationModel;
+}
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    protected pif: TabixIndexedFile;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getHeader(): Promise<string>;
+    getAssemblyNames(): string[];
+    hasDataForRefName(): Promise<boolean>;
+    getRefNames(opts?: BaseOptions & {
+        regions?: Region[];
+    }): Promise<string[]>;
+    getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -0,0 +1,107 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+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 SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
+class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const pifGzLoc = this.getConf('pifGzLocation');
+        const type = this.getConf(['index', 'indexType']);
+        const loc = this.getConf(['index', 'location']);
+        const pm = this.pluginManager;
+        this.pif = new tabix_1.TabixIndexedFile({
+            filehandle: (0, io_1.openLocation)(pifGzLoc, pm),
+            csiFilehandle: type === 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
+            tbiFilehandle: type !== 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+    }
+    async getHeader() {
+        return this.pif.getHeader();
+    }
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        if (assemblyNames.length === 0) {
+            return [
+                this.getConf('queryAssembly'),
+                this.getConf('targetAssembly'),
+            ];
+        }
+        return assemblyNames;
+    }
+    async hasDataForRefName() {
+        return true;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        if (!r1) {
+            throw new Error('no assembly name provided');
+        }
+        const idx = this.getAssemblyNames().indexOf(r1);
+        const names = await this.pif.getReferenceSequenceNames(opts);
+        if (idx === 0) {
+            return names.filter(n => n.startsWith('q')).map(n => n.slice(1));
+        }
+        else if (idx === 1) {
+            return names.filter(n => n.startsWith('t')).map(n => n.slice(1));
+        }
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { assemblyName } = query;
+            const assemblyNames = this.getAssemblyNames();
+            const index = assemblyNames.indexOf(assemblyName);
+            const flip = index === 0;
+            const letter = flip ? 'q' : 't';
+            await this.pif.getLines(letter + query.refName, query.start, query.end, {
+                lineCallback: (line, fileOffset) => {
+                    const r = (0, util_1.parsePAFLine)(line);
+                    const refName = r.qname.slice(1);
+                    const start = r.qstart;
+                    const end = r.qend;
+                    const mateName = r.tname;
+                    const mateStart = r.tstart;
+                    const mateEnd = r.tend;
+                    const { extra, strand } = r;
+                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
+                    observer.next(new SyntenyFeature_1.default({
+                        uniqueId: fileOffset + assemblyName,
+                        assemblyName,
+                        start,
+                        end,
+                        type: 'match',
+                        refName,
+                        strand,
+                        ...rest,
+                        CIGAR: extra.cg,
+                        syntenyId: fileOffset,
+                        identity: numMatches / blockLen,
+                        numMatches,
+                        blockLen,
+                        mate: {
+                            start: mateStart,
+                            end: mateEnd,
+                            refName: mateName,
+                            assemblyName: assemblyNames[+flip],
+                        },
+                    }));
+                },
+                signal: opts.signal,
+            });
+            observer.complete();
+        });
+    }
+    freeResources( /* { query } */) { }
+}
+PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
+exports.default = PAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -0,0 +1,61 @@
+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;
+        defaultValue: {
+            uri: string;
+            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: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PairwiseIndexedPAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/configSchema.js

@@ -0,0 +1,69 @@
+"use strict";
+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
+const PairwiseIndexedPAFAdapter = (0, configuration_1.ConfigurationSchema)('PairwiseIndexedPAFAdapter', {
+    /**
+     * #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
+     */
+    pifGzLocation: {
+        type: 'fileLocation',
+        description: 'location of pairwise tabix indexed PAF (pif)',
+        defaultValue: {
+            uri: '/path/to/data/file.pif.gz',
+            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: {
+                uri: '/path/to/my.paf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+}, { explicitlyTyped: true });
+exports.default = PairwiseIndexedPAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/index.d.ts

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

package/dist/PairwiseIndexedPAFAdapter/index.js

@@ -0,0 +1,41 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'PairwiseIndexedPAFAdapter',
+        displayName: 'Pairwise indexed PAF adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PairwiseIndexedPAFAdapter'))).then(r => r.default),
+    }));
+};

package/dist/index.js

@@ -5,6 +5,7 @@ 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 MCScanAnchorsAdapter_1 = __importDefault(require("./MCScanAnchorsAdapter"));
 const MCScanSimpleAnchorsAdapter_1 = __importDefault(require("./MCScanSimpleAnchorsAdapter"));
 const MashMapAdapter_1 = __importDefault(require("./MashMapAdapter"));
@@ -18,6 +19,7 @@ class ComparativeAdaptersPlugin extends Plugin_1.default {
     }
     install(pluginManager) {
         (0, PAFAdapter_1.default)(pluginManager);
+        (0, PairwiseIndexedPAFAdapter_1.default)(pluginManager);
         (0, DeltaAdapter_1.default)(pluginManager);
         (0, ChainAdapter_1.default)(pluginManager);
         (0, MCScanAnchorsAdapter_1.default)(pluginManager);
@@ -38,12 +40,9 @@ class ComparativeAdaptersPlugin extends Plugin_1.default {
             };
         });
         pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => {
-                if (adapterName === 'PAFAdapter') {
-                    return 'SyntenyTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
+            return (adapterName) => adapterName === 'PAFAdapter'
+                ? 'SyntenyTrack'
+                : trackTypeGuesser(adapterName);
         });
     }
 }

package/dist/util.d.ts

@@ -14,3 +14,6 @@ export declare function parseBed(text: string): Map<string, {
 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 parsePAFLine(line: string): PAFRecord;
+export declare function flipCigar(cigar: string[]): string[];
+export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseLineByLine = exports.zip = exports.readFile = exports.parseBed = exports.isGzip = void 0;
+exports.swapIndelCigar = exports.flipCigar = exports.parsePAFLine = exports.parseLineByLine = exports.zip = exports.readFile = exports.parseBed = exports.isGzip = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
@@ -54,3 +54,50 @@ function parseLineByLine(buffer, cb) {
     return entries;
 }
 exports.parseLineByLine = parseLineByLine;
+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,
+        },
+    };
+}
+exports.parsePAFLine = parsePAFLine;
+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;
+}
+exports.flipCigar = flipCigar;
+function swapIndelCigar(cigar) {
+    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
+}
+exports.swapIndelCigar = swapIndelCigar;

package/esm/PAFAdapter/PAFAdapter.js

@@ -6,9 +6,9 @@ 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';
+import SyntenyFeature from '../SyntenyFeature';
+import { flipCigar, swapIndelCigar, parsePAFLine, isGzip, parseLineByLine, } from '../util';
+import { getWeightedMeans } from './util';
 const { parseCigar } = MismatchParser;
 class PAFAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
@@ -70,8 +70,11 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             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;
+            const index = assemblyNames.indexOf(assemblyName);
+            // if the getFeatures::query is on the query assembly, flip orientation
+            // of data
+            const flip = index === 0;
             if (index === -1) {
                 console.warn(`${assemblyName} not found in this adapter`);
                 observer.complete();
@@ -84,9 +87,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                 let mateName = '';
                 let mateStart = 0;
                 let mateEnd = 0;
-                const flip = index === 0;
-                const assemblyName = assemblyNames[+!flip];
-                if (index === 0) {
+                if (flip) {
                     start = r.qstart;
                     end = r.qend;
                     refName = r.qname;

package/esm/PAFAdapter/util.d.ts

@@ -15,6 +15,3 @@ export interface PAFRecord {
     };
 }
 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

@@ -76,47 +76,3 @@ function weightedMean(tuples) {
     ], [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');
-}

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -0,0 +1,24 @@
+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';
+interface PAFOptions extends BaseOptions {
+    config?: AnyConfigurationModel;
+}
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    protected pif: TabixIndexedFile;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getHeader(): Promise<string>;
+    getAssemblyNames(): string[];
+    hasDataForRefName(): Promise<boolean>;
+    getRefNames(opts?: BaseOptions & {
+        regions?: Region[];
+    }): Promise<string[]>;
+    getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -0,0 +1,102 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { openLocation } from '@jbrowse/core/util/io';
+import { TabixIndexedFile } from '@gmod/tabix';
+// locals
+import { parsePAFLine } from '../util';
+import SyntenyFeature from '../SyntenyFeature';
+class PAFAdapter extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const pifGzLoc = this.getConf('pifGzLocation');
+        const type = this.getConf(['index', 'indexType']);
+        const loc = this.getConf(['index', 'location']);
+        const pm = this.pluginManager;
+        this.pif = new TabixIndexedFile({
+            filehandle: openLocation(pifGzLoc, pm),
+            csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
+            tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+    }
+    async getHeader() {
+        return this.pif.getHeader();
+    }
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        if (assemblyNames.length === 0) {
+            return [
+                this.getConf('queryAssembly'),
+                this.getConf('targetAssembly'),
+            ];
+        }
+        return assemblyNames;
+    }
+    async hasDataForRefName() {
+        return true;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        if (!r1) {
+            throw new Error('no assembly name provided');
+        }
+        const idx = this.getAssemblyNames().indexOf(r1);
+        const names = await this.pif.getReferenceSequenceNames(opts);
+        if (idx === 0) {
+            return names.filter(n => n.startsWith('q')).map(n => n.slice(1));
+        }
+        else if (idx === 1) {
+            return names.filter(n => n.startsWith('t')).map(n => n.slice(1));
+        }
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { assemblyName } = query;
+            const assemblyNames = this.getAssemblyNames();
+            const index = assemblyNames.indexOf(assemblyName);
+            const flip = index === 0;
+            const letter = flip ? 'q' : 't';
+            await this.pif.getLines(letter + query.refName, query.start, query.end, {
+                lineCallback: (line, fileOffset) => {
+                    const r = parsePAFLine(line);
+                    const refName = r.qname.slice(1);
+                    const start = r.qstart;
+                    const end = r.qend;
+                    const mateName = r.tname;
+                    const mateStart = r.tstart;
+                    const mateEnd = r.tend;
+                    const { extra, strand } = r;
+                    const { numMatches = 0, blockLen = 1, cg, ...rest } = extra;
+                    observer.next(new SyntenyFeature({
+                        uniqueId: fileOffset + assemblyName,
+                        assemblyName,
+                        start,
+                        end,
+                        type: 'match',
+                        refName,
+                        strand,
+                        ...rest,
+                        CIGAR: extra.cg,
+                        syntenyId: fileOffset,
+                        identity: numMatches / blockLen,
+                        numMatches,
+                        blockLen,
+                        mate: {
+                            start: mateStart,
+                            end: mateEnd,
+                            refName: mateName,
+                            assemblyName: assemblyNames[+flip],
+                        },
+                    }));
+                },
+                signal: opts.signal,
+            });
+            observer.complete();
+        });
+    }
+    freeResources( /* { query } */) { }
+}
+PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default PAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -0,0 +1,61 @@
+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;
+        defaultValue: {
+            uri: string;
+            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: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PairwiseIndexedPAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.js

@@ -0,0 +1,67 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+/**
+ * #config PairwiseIndexedPAFAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter', {
+    /**
+     * #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
+     */
+    pifGzLocation: {
+        type: 'fileLocation',
+        description: 'location of pairwise tabix indexed PAF (pif)',
+        defaultValue: {
+            uri: '/path/to/data/file.pif.gz',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    index: ConfigurationSchema('TabixIndex', {
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.paf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+}, { explicitlyTyped: true });
+export default PairwiseIndexedPAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/index.d.ts

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

package/esm/PairwiseIndexedPAFAdapter/index.js

@@ -0,0 +1,13 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'PairwiseIndexedPAFAdapter',
+        displayName: 'Pairwise indexed PAF adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./PairwiseIndexedPAFAdapter').then(r => r.default),
+    }));
+};

package/esm/index.js

@@ -1,5 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PAFAdapterF from './PAFAdapter';
+import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
 import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
 import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
 import MashMapAdapterF from './MashMapAdapter';
@@ -13,6 +14,7 @@ export default class ComparativeAdaptersPlugin extends Plugin {
     }
     install(pluginManager) {
         PAFAdapterF(pluginManager);
+        PairwiseIndexedPAFAdapterF(pluginManager);
         DeltaAdapterF(pluginManager);
         ChainAdapterF(pluginManager);
         MCScanAnchorsAdapterF(pluginManager);
@@ -33,12 +35,9 @@ export default class ComparativeAdaptersPlugin extends Plugin {
             };
         });
         pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => {
-                if (adapterName === 'PAFAdapter') {
-                    return 'SyntenyTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
+            return (adapterName) => adapterName === 'PAFAdapter'
+                ? 'SyntenyTrack'
+                : trackTypeGuesser(adapterName);
         });
     }
 }

package/esm/util.d.ts

@@ -14,3 +14,6 @@ export declare function parseBed(text: string): Map<string, {
 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 parsePAFLine(line: string): PAFRecord;
+export declare function flipCigar(cigar: string[]): string[];
+export declare function swapIndelCigar(cigar: string): string;

package/esm/util.js

@@ -46,3 +46,47 @@ export function parseLineByLine(buffer, cb) {
     }
     return entries;
 }
+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');
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.8.0",
+  "version": "2.10.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -37,6 +37,7 @@
   },
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.3",
+    "@gmod/tabix": "^1.5.6",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
@@ -58,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
+  "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
 }