@jbrowse/plugin-sequence 2.1.2 → 2.1.3

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,7 +1,7 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends IndexedFasta {
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    setupPre(): Promise<{
+        fasta: BgzipIndexedFasta;
+    }>;
 }

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -5,29 +5,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const indexedfasta_1 = require("@gmod/indexedfasta");
 const io_1 = require("@jbrowse/core/util/io");
-const configuration_1 = require("@jbrowse/core/configuration");
 const IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
 class default_1 extends IndexedFastaAdapter_1.default {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const fastaLocation = (0, configuration_1.readConfObject)(config, 'fastaLocation');
-        const faiLocation = (0, configuration_1.readConfObject)(config, 'faiLocation');
-        const gziLocation = (0, configuration_1.readConfObject)(config, 'gziLocation');
-        if (!fastaLocation) {
-            throw new Error('must provide fastaLocation');
-        }
-        if (!faiLocation) {
-            throw new Error('must provide faiLocation');
-        }
-        if (!gziLocation) {
-            throw new Error('must provide gziLocation');
-        }
+    async setupPre() {
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        const gziLocation = this.getConf('gziLocation');
         const fastaOpts = {
             fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
             fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
             gzi: (0, io_1.openLocation)(gziLocation, this.pluginManager),
         };
-        this.fasta = new indexedfasta_1.BgzipIndexedFasta(fastaOpts);
+        return { fasta: new indexedfasta_1.BgzipIndexedFasta(fastaOpts) };
     }
 }
 exports.default = default_1;

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"BgzipFastaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/BgzipFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAsD;AAEtD,8CAAoD;AACpD,+DAA4D;AAE5D,qGAAqE;AAIrE,eAAqB,SAAQ,6BAAY;IACvC,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,MAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,IAAI,CAAC,aAAa,EAAE;YAClB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;SAC9C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,MAAM,SAAS,GAAG;YAChB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAA6B,EAAE,IAAI,CAAC,aAAa,CAAC;YACtE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;YAClE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;SACnE,CAAA;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,gCAAiB,CAAC,SAAS,CAAC,CAAA;IAC/C,CAAC;CACF;AA3BD,4BA2BC"}
+{"version":3,"file":"BgzipFastaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/BgzipFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAsD;AAEtD,8CAAoD;AACpD,qGAAqE;AAErE,eAAqB,SAAQ,6BAAY;IAChC,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,SAAS,GAAG;YAChB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAA6B,EAAE,IAAI,CAAC,aAAa,CAAC;YACtE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;YAClE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;SACnE,CAAA;QAED,OAAO,EAAE,KAAK,EAAE,IAAI,gCAAiB,CAAC,SAAS,CAAC,EAAE,CAAA;IACpD,CAAC;CACF;AAbD,4BAaC"}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -6,8 +6,9 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseSequenceAdapter {
-    protected fasta: IndexedFasta;
-    protected header?: Promise<string>;
+    protected setupP?: Promise<{
+        fasta: IndexedFasta;
+    }>;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -16,7 +17,13 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
+    setupPre(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getHeader(): Promise<string | null>;
+    setup(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -16,49 +16,54 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
         this.seqCache = new abortable_promise_cache_1.default({
             cache: new QuickLRU_1.default({ maxSize: 200 }),
             fill: async (args, signal) => {
-                const { refName, start, end } = args;
-                return this.fasta.getSequence(refName, start, end, { ...args, signal });
+                const { refName, start, end, fasta } = args;
+                return fasta.getSequence(refName, start, end, { ...args, signal });
             },
         });
-        const fastaLocation = this.getConf('fastaLocation');
-        const faiLocation = this.getConf('faiLocation');
-        const fastaOpts = {
-            fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
-            fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
-        };
-        this.fasta = new indexedfasta_1.IndexedFasta(fastaOpts);
     }
-    getRefNames(opts) {
-        return this.fasta.getSequenceNames(opts);
+    async getRefNames(opts) {
+        const { fasta } = await this.setup();
+        return fasta.getSequenceNames(opts);
     }
     async getRegions(opts) {
-        const seqSizes = await this.fasta.getSequenceSizes(opts);
+        const { fasta } = await this.setup();
+        const seqSizes = await fasta.getSequenceSizes(opts);
         return Object.keys(seqSizes).map(refName => ({
             refName,
             start: 0,
             end: seqSizes[refName],
         }));
     }
+    async setupPre() {
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        return {
+            fasta: new indexedfasta_1.IndexedFasta({
+                fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
+                fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
+            }),
+        };
+    }
     async getHeader() {
-        if (this.header) {
-            return this.header;
-        }
         const loc = this.getConf('metadataLocation');
-        if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
-            return null;
+        return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
+            ? null
+            : (0, io_1.openLocation)(loc).readFile('utf8');
+    }
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        this.header = (0, io_1.openLocation)(loc)
-            .readFile('utf8')
-            .catch(e => {
-            this.header = undefined;
-            throw e;
-        });
-        return this.header;
+        return this.setupP;
     }
     getFeatures(region, opts) {
         const { refName, start, end } = region;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const size = await this.fasta.getSequenceSize(refName, opts);
+            const { fasta } = await this.setup();
+            const size = await fasta.getSequenceSize(refName, opts);
             const regionEnd = size !== undefined ? Math.min(size, end) : end;
             const chunks = [];
             const chunkSize = 128000;
@@ -70,7 +75,7 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
                     start: chunkStart,
                     end: chunkStart + chunkSize,
                 };
-                chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                chunks.push(this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts === null || opts === void 0 ? void 0 : opts.signal));
             }
             const seq = (await Promise.all(chunks))
                 .join('')

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAiD;AACjD,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAA2D;AAE3D,sFAA2D;AAC3D,2EAAkD;AAMlD,eAAqB,SAAQ,iCAAmB;IAW9C,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAbrC,aAAQ,GAAG,IAAI,iCAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,kBAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAQF,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,2BAAY,CAAC;gBACtB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA1GD,4BA0GC"}

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,7 +1,7 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends IndexedFasta {
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    setupPre(): Promise<{
+        fasta: BgzipIndexedFasta;
+    }>;
 }

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,28 +1,17 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import { openLocation } from '@jbrowse/core/util/io';
-import { readConfObject } from '@jbrowse/core/configuration';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
 export default class extends IndexedFasta {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const fastaLocation = readConfObject(config, 'fastaLocation');
-        const faiLocation = readConfObject(config, 'faiLocation');
-        const gziLocation = readConfObject(config, 'gziLocation');
-        if (!fastaLocation) {
-            throw new Error('must provide fastaLocation');
-        }
-        if (!faiLocation) {
-            throw new Error('must provide faiLocation');
-        }
-        if (!gziLocation) {
-            throw new Error('must provide gziLocation');
-        }
+    async setupPre() {
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        const gziLocation = this.getConf('gziLocation');
         const fastaOpts = {
             fasta: openLocation(fastaLocation, this.pluginManager),
             fai: openLocation(faiLocation, this.pluginManager),
             gzi: openLocation(gziLocation, this.pluginManager),
         };
-        this.fasta = new BgzipIndexedFasta(fastaOpts);
+        return { fasta: new BgzipIndexedFasta(fastaOpts) };
     }
 }
 //# sourceMappingURL=BgzipFastaAdapter.js.map

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BgzipFastaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/BgzipFastaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,YAAY,MAAM,4CAA4C,CAAA;AAErE,MAAM,CAAC,OAAO,MAAO,SAAQ,YAAY;IAChC,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,SAAS,GAAG;YAChB,KAAK,EAAE,YAAY,CAAC,aAA6B,EAAE,IAAI,CAAC,aAAa,CAAC;YACtE,GAAG,EAAE,YAAY,CAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;YAClE,GAAG,EAAE,YAAY,CAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;SACnE,CAAA;QAED,OAAO,EAAE,KAAK,EAAE,IAAI,iBAAiB,CAAC,SAAS,CAAC,EAAE,CAAA;IACpD,CAAC;CACF"}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -6,8 +6,9 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseSequenceAdapter {
-    protected fasta: IndexedFasta;
-    protected header?: Promise<string>;
+    protected setupP?: Promise<{
+        fasta: IndexedFasta;
+    }>;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -16,7 +17,13 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
+    setupPre(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getHeader(): Promise<string | null>;
+    setup(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -4,56 +4,61 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature } from '@jbrowse/core/util';
 import AbortablePromiseCache from 'abortable-promise-cache';
-import LRU from '@jbrowse/core/util/QuickLRU';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 export default class extends BaseSequenceAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.seqCache = new AbortablePromiseCache({
-            cache: new LRU({ maxSize: 200 }),
+            cache: new QuickLRU({ maxSize: 200 }),
             fill: async (args, signal) => {
-                const { refName, start, end } = args;
-                return this.fasta.getSequence(refName, start, end, { ...args, signal });
+                const { refName, start, end, fasta } = args;
+                return fasta.getSequence(refName, start, end, { ...args, signal });
             },
         });
-        const fastaLocation = this.getConf('fastaLocation');
-        const faiLocation = this.getConf('faiLocation');
-        const fastaOpts = {
-            fasta: openLocation(fastaLocation, this.pluginManager),
-            fai: openLocation(faiLocation, this.pluginManager),
-        };
-        this.fasta = new IndexedFasta(fastaOpts);
     }
-    getRefNames(opts) {
-        return this.fasta.getSequenceNames(opts);
+    async getRefNames(opts) {
+        const { fasta } = await this.setup();
+        return fasta.getSequenceNames(opts);
     }
     async getRegions(opts) {
-        const seqSizes = await this.fasta.getSequenceSizes(opts);
+        const { fasta } = await this.setup();
+        const seqSizes = await fasta.getSequenceSizes(opts);
         return Object.keys(seqSizes).map(refName => ({
             refName,
             start: 0,
             end: seqSizes[refName],
         }));
     }
+    async setupPre() {
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        return {
+            fasta: new IndexedFasta({
+                fasta: openLocation(fastaLocation, this.pluginManager),
+                fai: openLocation(faiLocation, this.pluginManager),
+            }),
+        };
+    }
     async getHeader() {
-        if (this.header) {
-            return this.header;
-        }
         const loc = this.getConf('metadataLocation');
-        if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
-            return null;
+        return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
+            ? null
+            : openLocation(loc).readFile('utf8');
+    }
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        this.header = openLocation(loc)
-            .readFile('utf8')
-            .catch(e => {
-            this.header = undefined;
-            throw e;
-        });
-        return this.header;
+        return this.setupP;
     }
     getFeatures(region, opts) {
         const { refName, start, end } = region;
         return ObservableCreate(async (observer) => {
-            const size = await this.fasta.getSequenceSize(refName, opts);
+            const { fasta } = await this.setup();
+            const size = await fasta.getSequenceSize(refName, opts);
             const regionEnd = size !== undefined ? Math.min(size, end) : end;
             const chunks = [];
             const chunkSize = 128000;
@@ -65,7 +70,7 @@ export default class extends BaseSequenceAdapter {
                     start: chunkStart,
                     end: chunkStart + chunkSize,
                 };
-                chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                chunks.push(this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts === null || opts === void 0 ? void 0 : opts.signal));
             }
             const seq = (await Promise.all(chunks))
                 .join('')

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EACL,mBAAmB,GAEpB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAW,MAAM,oBAAoB,CAAA;AAE3D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAMlD,MAAM,CAAC,OAAO,MAAO,SAAQ,mBAAmB;IAW9C,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAbrC,aAAQ,GAAG,IAAI,qBAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAQF,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,YAAY,CAAC;gBACtB,KAAK,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,YAAY,CAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.1.2",
+  "version": "2.1.3",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -59,5 +59,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
+  "gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
 }

package/src/BgzipFastaAdapter/BgzipFastaAdapter.ts

@@ -1,37 +1,19 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta'
 import { FileLocation } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends IndexedFasta {
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const fastaLocation = readConfObject(config, 'fastaLocation')
-    const faiLocation = readConfObject(config, 'faiLocation')
-    const gziLocation = readConfObject(config, 'gziLocation')
-    if (!fastaLocation) {
-      throw new Error('must provide fastaLocation')
-    }
-    if (!faiLocation) {
-      throw new Error('must provide faiLocation')
-    }
-    if (!gziLocation) {
-      throw new Error('must provide gziLocation')
-    }
+  public async setupPre() {
+    const fastaLocation = this.getConf('fastaLocation')
+    const faiLocation = this.getConf('faiLocation')
+    const gziLocation = this.getConf('gziLocation')
     const fastaOpts = {
       fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
       fai: openLocation(faiLocation as FileLocation, this.pluginManager),
       gzi: openLocation(gziLocation as FileLocation, this.pluginManager),
     }
 
-    this.fasta = new BgzipIndexedFasta(fastaOpts)
+    return { fasta: new BgzipIndexedFasta(fastaOpts) }
   }
 }

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -9,23 +9,20 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { SimpleFeature, Feature } from '@jbrowse/core/util'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import AbortablePromiseCache from 'abortable-promise-cache'
-import LRU from '@jbrowse/core/util/QuickLRU'
+import QuickLRU from '@jbrowse/core/util/QuickLRU'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
-export default class extends BaseSequenceAdapter {
-  protected fasta: IndexedFasta
+type T = { refName: string; start: number; end: number; fasta: IndexedFasta }
 
-  protected header?: Promise<string>
+export default class extends BaseSequenceAdapter {
+  protected setupP?: Promise<{ fasta: IndexedFasta }>
 
-  private seqCache = new AbortablePromiseCache({
-    cache: new LRU({ maxSize: 200 }),
-    fill: async (
-      args: { refName: string; start: number; end: number },
-      signal?: AbortSignal,
-    ) => {
-      const { refName, start, end } = args
-      return this.fasta.getSequence(refName, start, end, { ...args, signal })
+  private seqCache = new AbortablePromiseCache<T, string | undefined>({
+    cache: new QuickLRU({ maxSize: 200 }),
+    fill: async (args: T, signal?: AbortSignal) => {
+      const { refName, start, end, fasta } = args
+      return fasta.getSequence(refName, start, end, { ...args, signal })
     },
   })
 
@@ -35,22 +32,16 @@ export default class extends BaseSequenceAdapter {
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const fastaLocation = this.getConf('fastaLocation')
-    const faiLocation = this.getConf('faiLocation')
-    const fastaOpts = {
-      fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
-      fai: openLocation(faiLocation as FileLocation, this.pluginManager),
-    }
-
-    this.fasta = new IndexedFasta(fastaOpts)
   }
 
-  public getRefNames(opts?: BaseOptions) {
-    return this.fasta.getSequenceNames(opts)
+  public async getRefNames(opts?: BaseOptions) {
+    const { fasta } = await this.setup()
+    return fasta.getSequenceNames(opts)
   }
 
   public async getRegions(opts?: BaseOptions) {
-    const seqSizes = await this.fasta.getSequenceSizes(opts)
+    const { fasta } = await this.setup()
+    const seqSizes = await fasta.getSequenceSizes(opts)
     return Object.keys(seqSizes).map(refName => ({
       refName,
       start: 0,
@@ -58,30 +49,40 @@ export default class extends BaseSequenceAdapter {
     }))
   }
 
-  public async getHeader() {
-    if (this.header) {
-      return this.header
-    }
-    const loc = this.getConf('metadataLocation')
+  public async setupPre() {
+    const fastaLocation = this.getConf('fastaLocation') as FileLocation
+    const faiLocation = this.getConf('faiLocation') as FileLocation
 
-    if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
-      return null
+    return {
+      fasta: new IndexedFasta({
+        fasta: openLocation(fastaLocation, this.pluginManager),
+        fai: openLocation(faiLocation, this.pluginManager),
+      }),
     }
+  }
 
-    this.header = openLocation(loc)
-      .readFile('utf8')
-      .catch(e => {
-        this.header = undefined
+  public async getHeader() {
+    const loc = this.getConf('metadataLocation')
+    return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
+      ? null
+      : openLocation(loc).readFile('utf8')
+  }
+
+  public async setup() {
+    if (!this.setupP) {
+      this.setupP = this.setupPre().catch(e => {
+        this.setupP = undefined
         throw e
       })
-
-    return this.header
+    }
+    return this.setupP
   }
 
   public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {
     const { refName, start, end } = region
     return ObservableCreate<Feature>(async observer => {
-      const size = await this.fasta.getSequenceSize(refName, opts)
+      const { fasta } = await this.setup()
+      const size = await fasta.getSequenceSize(refName, opts)
       const regionEnd = size !== undefined ? Math.min(size, end) : end
       const chunks = []
       const chunkSize = 128000
@@ -94,7 +95,9 @@ export default class extends BaseSequenceAdapter {
           start: chunkStart,
           end: chunkStart + chunkSize,
         }
-        chunks.push(this.seqCache.get(JSON.stringify(r), r, opts?.signal))
+        chunks.push(
+          this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts?.signal),
+        )
       }
       const seq = (await Promise.all(chunks))
         .join('')

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@jbrowse/core/util/QuickLRU'