@jbrowse/plugin-comparative-adapters 2.6.1

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -0,0 +1,121 @@
+"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 io_1 = require("@jbrowse/core/util/io");
+const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const util_2 = require("../util");
+class MCScanAnchorsAdapter extends BaseAdapter_1.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 assemblyNames = this.getConf('assemblyNames');
+        const pm = this.pluginManager;
+        const bed1 = (0, io_1.openLocation)(this.getConf('bed1Location'), pm);
+        const bed2 = (0, io_1.openLocation)(this.getConf('bed2Location'), pm);
+        const mcscan = (0, io_1.openLocation)(this.getConf('mcscanSimpleAnchorsLocation'), pm);
+        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts)));
+        const bed1Map = (0, util_2.parseBed)(bed1text);
+        const bed2Map = (0, util_2.parseBed)(bed2text);
+        const feats = mcscantext
+            .split(/\n|\r\n|\r/)
+            .filter(f => !!f && f !== '###')
+            .map((line, index) => {
+            const [n11, n12, n21, n22, score, strand] = line.split('\t');
+            const r11 = bed1Map.get(n11);
+            const r12 = bed1Map.get(n12);
+            const r21 = bed2Map.get(n21);
+            const r22 = bed2Map.get(n22);
+            if (!r11 || !r12 || !r21 || !r22) {
+                throw new Error(`feature not found, ${n11} ${n12} ${n21} ${n22} ${r11} ${r12} ${r21} ${r22}`);
+            }
+            return [
+                r11,
+                r12,
+                r21,
+                r22,
+                +score,
+                strand === '-' ? -1 : 1,
+                index,
+            ];
+        });
+        return {
+            assemblyNames,
+            feats,
+        };
+    }
+    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 (BaseFeatureDataAdapter filters it out)
+        return true;
+    }
+    async getRefNames() {
+        // we cannot determine this accurately
+        return [];
+    }
+    getFeatures(region, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { assemblyNames, feats } = await this.setup(opts);
+            // The index of the assembly name in the region list corresponds to
+            // the adapter in the subadapters list
+            const index = assemblyNames.indexOf(region.assemblyName);
+            if (index !== -1) {
+                const flip = index === 0;
+                feats.forEach(f => {
+                    const [f11, f12, f21, f22, score, strand, rowNum] = f;
+                    let r1 = {
+                        refName: f11.refName,
+                        start: Math.min(f11.start, f12.start),
+                        end: Math.max(f11.end, f12.end),
+                    };
+                    let r2 = {
+                        refName: f21.refName,
+                        start: Math.min(f21.start, f22.start),
+                        end: Math.max(f21.end, f22.end),
+                    };
+                    if (!flip) {
+                        ;
+                        [r2, r1] = [r1, r2];
+                    }
+                    if (r1.refName === region.refName &&
+                        (0, util_1.doesIntersect2)(r1.start, r1.end, region.start, region.end)) {
+                        observer.next(new simpleFeature_1.default({
+                            ...r1,
+                            uniqueId: `${rowNum}`,
+                            syntenyId: rowNum,
+                            assemblyName: assemblyNames[+!flip],
+                            score,
+                            strand,
+                            mate: {
+                                ...r2,
+                                assemblyName: assemblyNames[+flip],
+                            },
+                        }));
+                    }
+                });
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * 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( /* { region } */) { }
+}
+MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
+exports.default = MCScanAnchorsAdapter;
+//# sourceMappingURL=MCScanSimpleAnchorsAdapter.js.map

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MCScanSimpleAnchorsAdapter/configSchema.d.ts

@@ -0,0 +1,40 @@
+declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    mcscanSimpleAnchorsLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    bed1Location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    bed2Location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default MCScanSimpleAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -0,0 +1,48 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config MCScanSimpleAnchorsAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const MCScanSimpleAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanSimpleAnchorsAdapter', {
+    /**
+     * #slot
+     */
+    mcscanSimpleAnchorsLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/mcscan.anchors.simple',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    bed1Location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/file.bed',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    bed2Location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/file.bed',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+exports.default = MCScanSimpleAnchorsAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/MCScanSimpleAnchorsAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MCScanSimpleAnchorsAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,0BAA0B,GAAG,IAAA,mCAAmB,EACpD,4BAA4B,EAC5B;IACE;;OAEG;IACH,2BAA2B,EAAE;QAC3B,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gCAAgC;YACrC,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,mBAAmB;YACxB,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,mBAAmB;YACxB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,0BAA0B,CAAA"}

package/dist/MCScanSimpleAnchorsAdapter/index.d.ts

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

package/dist/MCScanSimpleAnchorsAdapter/index.js

@@ -0,0 +1,42 @@
+"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: 'MCScanSimpleAnchorsAdapter',
+        displayName: 'MCScan anchors.simple adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanSimpleAnchorsAdapter'))).then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/dist/MCScanSimpleAnchorsAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MCScanSimpleAnchorsAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,4BAA4B;QAClC,WAAW,EAAE,+BAA+B;QAC5C,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,8BAA8B,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KAC9D,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/MashMapAdapter/MashMapAdapter.d.ts

@@ -0,0 +1,5 @@
+import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+export default class MashMapAdapter extends PAFAdapter {
+    setupPre(opts?: BaseOptions): Promise<import("../PAFAdapter/util").PAFRecord[]>;
+}

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -0,0 +1,42 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const io_1 = require("@jbrowse/core/util/io");
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
+const util_1 = require("../util");
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+class MashMapAdapter extends PAFAdapter_1.default {
+    async setupPre(opts) {
+        const outLoc = (0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager);
+        const buffer = (await outLoc.readFile(opts));
+        const buf = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        return (0, util_1.parseLineByLine)(buf, parseMashMapLine);
+    }
+}
+exports.default = MashMapAdapter;
+function parseMashMapLine(line) {
+    const fields = line.split(' ');
+    if (fields.length < 9) {
+        // xref https://github.com/marbl/MashMap/issues/38
+        throw new Error('improperly formatted line: ' + line);
+    }
+    const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;
+    return {
+        tname,
+        tstart: +tstart,
+        tend: +tend,
+        qname,
+        qstart: +qstart,
+        qend: +qend,
+        strand: strand === '-' ? -1 : 1,
+        extra: {
+            mappingQual: +mq,
+        },
+    };
+}
+//# sourceMappingURL=MashMapAdapter.js.map

package/dist/MashMapAdapter/MashMapAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MashMapAdapter/configSchema.d.ts

@@ -0,0 +1,37 @@
+declare const MashMapAdapter: 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
+     */
+    outLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default MashMapAdapter;

package/dist/MashMapAdapter/configSchema.js

@@ -0,0 +1,45 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config MashMapAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const MashMapAdapter = (0, configuration_1.ConfigurationSchema)('MashMapAdapter', {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Target is the first value in the array, query is the second',
+    },
+    /**
+     * #slot
+     */
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the target assembly',
+    },
+    /**
+     * #slot
+     */
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames array: the query assembly',
+    },
+    /**
+     * #slot
+     */
+    outLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/mashmap.out',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+exports.default = MashMapAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/MashMapAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MashMapAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,IAAA,mCAAmB,EACxC,gBAAgB,EAChB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EACT,6DAA6D;KAChE;IAED;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,yDAAyD;KACvE;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,wDAAwD;KACtE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,sBAAsB;YAC3B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,cAAc,CAAA"}

package/dist/MashMapAdapter/index.d.ts

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

package/dist/MashMapAdapter/index.js

@@ -0,0 +1,42 @@
+"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: 'MashMapAdapter',
+        displayName: 'MashMap adapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MashMapAdapter'))).then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/dist/MashMapAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MashMapAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,gBAAgB;QACtB,WAAW,EAAE,iBAAiB;QAC9B,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,kBAAkB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACvE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/PAFAdapter/PAFAdapter.d.ts

@@ -0,0 +1,20 @@
+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 { PAFRecord } from './util';
+interface PAFOptions extends BaseOptions {
+    config?: AnyConfigurationModel;
+}
+export default class PAFAdapter extends BaseFeatureDataAdapter {
+    private setupP?;
+    static capabilities: string[];
+    setup(opts?: BaseOptions): Promise<PAFRecord[]>;
+    setupPre(opts?: BaseOptions): Promise<PAFRecord[]>;
+    hasDataForRefName(): Promise<boolean>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/dist/PAFAdapter/PAFAdapter.js

@@ -0,0 +1,152 @@
+"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 range_1 = require("@jbrowse/core/util/range");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+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 util_1 = require("../util");
+const util_2 = require("./util");
+const { parseCigar } = plugin_alignments_1.MismatchParser;
+class PAFAdapter extends BaseAdapter_1.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 = (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);
+    }
+    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 (0, rxjs_1.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 && (0, configuration_1.readConfObject)(config, 'colorBy') === 'meanQueryIdentity') {
+                pafRecords = (0, util_2.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 && (0, range_1.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 = (0, util_2.flipCigar)(parseCigar(extra.cg)).join('');
+                        }
+                        else if (flip) {
+                            CIGAR = (0, util_2.swapIndelCigar)(extra.cg);
+                        }
+                    }
+                    observer.next(new SyntenyFeature_1.default({
+                        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'];
+exports.default = PAFAdapter;
+//# sourceMappingURL=PAFAdapter.js.map

package/dist/PAFAdapter/PAFAdapter.js.map

@@ -0,0 +1 @@
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