@jbrowse/plugin-comparative-adapters 2.6.1

package/esm/MCScanAnchorsAdapter/configSchema.js

@@ -0,0 +1,46 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config MCScanAnchorsAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
+    /**
+     * #slot
+     */
+    mcscanAnchorsLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/mcscan.anchors',
+            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 });
+export default MCScanAnchorsAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/MCScanAnchorsAdapter/configSchema.js.map

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

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

package/esm/MCScanAnchorsAdapter/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: 'MCScanAnchorsAdapter',
+        displayName: 'MCScan anchors adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./MCScanAnchorsAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/MCScanAnchorsAdapter/index.js.map

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

@@ -0,0 +1,41 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+interface BareFeature {
+    refName: string;
+    start: number;
+    end: number;
+    score: number;
+    name: string;
+}
+type Row = [
+    BareFeature,
+    BareFeature,
+    BareFeature,
+    BareFeature,
+    number,
+    number,
+    number
+];
+export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+    private setupP?;
+    static capabilities: string[];
+    setup(opts: BaseOptions): Promise<{
+        assemblyNames: string[];
+        feats: Row[];
+    }>;
+    setupPre(opts: BaseOptions): Promise<{
+        assemblyNames: string[];
+        feats: Row[];
+    }>;
+    hasDataForRefName(): Promise<boolean>;
+    getRefNames(): Promise<never[]>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the foreseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}
+export {};

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -0,0 +1,116 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { doesIntersect2 } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { readFile, parseBed } from '../util';
+class MCScanAnchorsAdapter 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 assemblyNames = this.getConf('assemblyNames');
+        const pm = this.pluginManager;
+        const bed1 = openLocation(this.getConf('bed1Location'), pm);
+        const bed2 = openLocation(this.getConf('bed2Location'), pm);
+        const mcscan = openLocation(this.getConf('mcscanSimpleAnchorsLocation'), pm);
+        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => readFile(r, opts)));
+        const bed1Map = parseBed(bed1text);
+        const bed2Map = 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 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 &&
+                        doesIntersect2(r1.start, r1.end, region.start, region.end)) {
+                        observer.next(new SimpleFeature({
+                            ...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'];
+export default MCScanAnchorsAdapter;
+//# sourceMappingURL=MCScanSimpleAnchorsAdapter.js.map

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -0,0 +1,46 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config MCScanSimpleAnchorsAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const MCScanSimpleAnchorsAdapter = 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 });
+export default MCScanSimpleAnchorsAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/MCScanSimpleAnchorsAdapter/configSchema.js.map

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

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

package/esm/MCScanSimpleAnchorsAdapter/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: 'MCScanSimpleAnchorsAdapter',
+        displayName: 'MCScan anchors.simple adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./MCScanSimpleAnchorsAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/MCScanSimpleAnchorsAdapter/index.js.map

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

package/esm/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/esm/MashMapAdapter/MashMapAdapter.js

@@ -0,0 +1,36 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { unzip } from '@gmod/bgzf-filehandle';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { parseLineByLine } from '../util';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class MashMapAdapter extends PAFAdapter {
+    async setupPre(opts) {
+        const outLoc = openLocation(this.getConf('outLocation'), this.pluginManager);
+        const buffer = (await outLoc.readFile(opts));
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        return parseLineByLine(buf, parseMashMapLine);
+    }
+}
+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/esm/MashMapAdapter/MashMapAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MashMapAdapter.js","sourceRoot":"","sources":["../../src/MashMapAdapter/MashMapAdapter.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,UAAU,MAAM,0BAA0B,CAAA;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,SAAS,CAAA;AAEzC,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,UAAU;IACpD,KAAK,CAAC,QAAQ,CAAC,IAAkB;QAC/B,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;QAC5E,MAAM,MAAM,GAAG,CAAC,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;QACtD,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACzD,OAAO,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;IAC/C,CAAC;CACF;AAED,SAAS,gBAAgB,CAAC,IAAY;IACpC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC9B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,kDAAkD;QAClD,MAAM,IAAI,KAAK,CAAC,6BAA6B,GAAG,IAAI,CAAC,CAAA;KACtD;IACD,MAAM,CAAC,KAAK,EAAE,AAAD,EAAG,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,AAAD,EAAG,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC,GAAG,MAAM,CAAA;IAEzE,OAAO;QACL,KAAK;QACL,MAAM,EAAE,CAAC,MAAM;QACf,IAAI,EAAE,CAAC,IAAI;QACX,KAAK;QACL,MAAM,EAAE,CAAC,MAAM;QACf,IAAI,EAAE,CAAC,IAAI;QACX,MAAM,EAAE,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC/B,KAAK,EAAE;YACL,WAAW,EAAE,CAAC,EAAE;SACjB;KACF,CAAA;AACH,CAAC"}

package/esm/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/esm/MashMapAdapter/configSchema.js

@@ -0,0 +1,43 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config MashMapAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const MashMapAdapter = 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 });
+export default MashMapAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/MashMapAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MashMapAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,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,eAAe,cAAc,CAAA"}

package/esm/MashMapAdapter/index.d.ts

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

package/esm/MashMapAdapter/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: 'MashMapAdapter',
+        displayName: 'MashMap adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/MashMapAdapter/index.js.map

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

package/esm/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 {};