@jbrowse/plugin-variants 1.7.0 → 1.7.1

package/dist/VcfTabixAdapter/VcfFeature.d.ts

@@ -1,59 +1,59 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-/**
- * VCF Feature creation with lazy genotype evaluation.
- */
-interface Samples {
-    [key: string]: {
-        [key: string]: {
-            values: string[] | number[] | null;
-        };
-    };
-}
-interface FeatureData {
-    [key: string]: unknown;
-    refName: string;
-    start: number;
-    end: number;
-    description?: string;
-    type?: string;
-    name?: string;
-    aliases?: string[];
-    samples?: Samples;
-}
-export default class VCFFeature implements Feature {
-    private variant;
-    private parser;
-    private data;
-    private _id;
-    constructor(args: {
-        variant: any;
-        parser: any;
-        id: string;
-    });
-    get(field: string): any;
-    set(): void;
-    parent(): undefined;
-    children(): undefined;
-    tags(): string[];
-    id(): string;
-    dataFromVariant(variant: {
-        REF: string;
-        POS: number;
-        ALT: string[];
-        CHROM: string;
-        INFO: any;
-        ID: string[];
-    }): FeatureData;
-    /**
-     * Get a sequence ontology (SO) term that describes the variant type
-     */
-    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
-    static _altTypeToSO: {
-        [key: string]: string | undefined;
-    };
-    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
-    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
-    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
-    toJSON(): any;
-}
-export {};
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+/**
+ * VCF Feature creation with lazy genotype evaluation.
+ */
+interface Samples {
+    [key: string]: {
+        [key: string]: {
+            values: string[] | number[] | null;
+        };
+    };
+}
+interface FeatureData {
+    [key: string]: unknown;
+    refName: string;
+    start: number;
+    end: number;
+    description?: string;
+    type?: string;
+    name?: string;
+    aliases?: string[];
+    samples?: Samples;
+}
+export default class VCFFeature implements Feature {
+    private variant;
+    private parser;
+    private data;
+    private _id;
+    constructor(args: {
+        variant: any;
+        parser: any;
+        id: string;
+    });
+    get(field: string): any;
+    set(): void;
+    parent(): undefined;
+    children(): undefined;
+    tags(): string[];
+    id(): string;
+    dataFromVariant(variant: {
+        REF: string;
+        POS: number;
+        ALT: string[];
+        CHROM: string;
+        INFO: any;
+        ID: string[];
+    }): FeatureData;
+    /**
+     * Get a sequence ontology (SO) term that describes the variant type
+     */
+    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
+    static _altTypeToSO: {
+        [key: string]: string | undefined;
+    };
+    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
+    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
+    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
+    toJSON(): any;
+}
+export {};

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,35 +1,35 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { TabixIndexedFile } from '@gmod/tabix';
-import VcfParser from '@gmod/vcf';
-import { GenericFilehandle } from 'generic-filehandle';
-export default class extends BaseFeatureDataAdapter {
-    private configured?;
-    private configurePre;
-    protected configure(): Promise<{
-        filehandle: GenericFilehandle;
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<any>;
-    getHeader(): Promise<string>;
-    getMetadata(): Promise<any>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import VcfParser from '@gmod/vcf';
+import { GenericFilehandle } from 'generic-filehandle';
+export default class extends BaseFeatureDataAdapter {
+    private configured?;
+    private configurePre;
+    protected configure(): Promise<{
+        filehandle: GenericFilehandle;
+        vcf: TabixIndexedFile;
+        parser: VcfParser;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getMetadata(): Promise<any>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * Checks if the data source has data for the given reference sequence,
+     * and then gets the features in the region if it does
+     *
+     * Currently this just calls getFeatureInRegion for each region. Adapters that
+     * are frequently called on multiple regions simultaneously may want to
+     * implement a more efficient custom version of this method.
+     *
+     * Also includes a bit of extra logging to warn when fetching a large portion
+     * of a VCF
+     * @param regions - Regions
+     * @param opts - Feature adapter options
+     * @returns Observable of Feature objects in the regions
+     */
+    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/VcfTabixAdapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/index.d.ts

@@ -1,7 +1,7 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-export default class VariantsPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
-export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class VariantsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}
+export { default as VcfFeature } from './VcfTabixAdapter/VcfFeature';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.7.0",
+  "version": "1.7.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -29,7 +29,8 @@
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
@@ -55,5 +56,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
+  "gitHead": "6da232090c90f22ac96fd464c33082c89b8da14b"
 }

package/dist/LinearVariantDisplay/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/VariantFeatureWidget/VariantFeatureWidget.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/index.test.d.ts

@@ -1 +0,0 @@
-export {};