@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/BamAdapter/configSchema.d.ts

@@ -1,2 +1,51 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    bamLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    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>>;
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/CramAdapter/CramAdapter.d.ts

@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/CramAdapter/CramAdapter.js

@@ -1,6 +1,6 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal } from '@jbrowse/core/util';
+import { checkAbortSignal, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
@@ -87,33 +87,33 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const conf = await this.configure();
-        statusCallback('Downloading index');
-        const { cram } = conf;
-        const samHeader = await cram.cram.getSamHeader();
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ID numbers and names
-        const idToName = [];
-        const nameToId = {};
-        samHeader
-            .filter(l => l.tag === 'SQ')
-            .forEach((sqLine, refId) => {
-            sqLine.data.forEach(item => {
-                if (item.tag === 'SN') {
-                    // this is the ref name
-                    const refName = item.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
+        return updateStatus('Downloading index', statusCallback, async () => {
+            const conf = await this.configure();
+            const { cram } = conf;
+            const samHeader = await cram.cram.getSamHeader();
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ID numbers and names
+            const idToName = [];
+            const nameToId = {};
+            samHeader
+                .filter(l => l.tag === 'SQ')
+                .forEach((sqLine, refId) => {
+                sqLine.data.forEach(item => {
+                    if (item.tag === 'SN') {
+                        // this is the ref name
+                        const refName = item.value;
+                        nameToId[refName] = refId;
+                        idToName[refId] = refName;
+                    }
+                });
             });
+            const readGroups = samHeader
+                .filter(l => l.tag === 'RG')
+                .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
+            const data = { idToName, nameToId, readGroups };
+            this.samHeader = data;
+            return { samHeader: data, ...conf };
         });
-        const readGroups = samHeader
-            .filter(l => l.tag === 'RG')
-            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
-        const data = { idToName, nameToId, readGroups };
-        statusCallback('');
-        this.samHeader = data;
-        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -165,29 +165,31 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             if (originalRefName) {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
-            statusCallback('Downloading alignments');
-            const records = await cram.getRecordsForRange(refId, start, end);
+            const records = await updateStatus('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
             checkAbortSignal(signal);
-            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-            let filtered = records.filter(record => {
-                const flags = record.flags;
-                return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-            });
-            if (tagFilter) {
-                filtered = filtered.filter(record => {
-                    // @ts-expect-error
-                    const val = record[tagFilter.tag];
-                    return val === '*' ? val !== undefined : val === tagFilter.value;
-                });
-            }
-            if (readName) {
-                filtered = filtered.filter(record => record.readName === readName);
-            }
-            filtered.forEach(record => {
-                observer.next(this.cramRecordToFeature(record));
+            await updateStatus('Processing alignments', statusCallback, () => {
+                var _a;
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                for (const record of records) {
+                    const flags = record.flags;
+                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                        continue;
+                    }
+                    if (tagFilter) {
+                        const v = tagFilter.tag === 'RG'
+                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            : record.tags[tagFilter.tag];
+                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                            continue;
+                        }
+                    }
+                    if (readName && record.readName !== readName) {
+                        continue;
+                    }
+                    observer.next(this.cramRecordToFeature(record));
+                }
+                observer.complete();
             });
-            statusCallback('');
-            observer.complete();
         }, signal);
     }
     freeResources( /* { region } */) { }
@@ -195,7 +197,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return new CramSlightlyLazyFeature(record, this);
     }
     // we return the configured fetchSizeLimit, and the bytes for the region
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
         return {

package/esm/CramAdapter/CramAdapter.js.map

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package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -32,8 +32,8 @@ export default class CramSlightlyLazyFeature {
         return this.record.isReverseComplemented() ? -1 : 1;
     }
     _read_group_id() {
-        const rg = this._store.samHeader.readGroups;
-        return rg ? rg[this.record.readGroupId] : undefined;
+        var _a;
+        return (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
     }
     _get_qual() {
         return (this.record.qualityScores || []).join(' ');
@@ -112,9 +112,7 @@ export default class CramSlightlyLazyFeature {
     _get_clipPos() {
         const mismatches = this.get('mismatches');
         if (mismatches.length) {
-            const record = this.get('strand') === -1
-                ? mismatches[mismatches.length - 1]
-                : mismatches[0];
+            const record = this.get('strand') === -1 ? mismatches.at(-1) : mismatches[0];
             const { type, cliplen } = record;
             if (type === 'softclip' || type === 'hardclip') {
                 return cliplen;

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
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package/esm/CramAdapter/CramTestAdapters.js

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ConfigurationSchema } from '@jbrowse/core/configuration/configurationSchema';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
 // setup for Cram Adapter Testing
 export function parseSmallFasta(text) {
     return text
@@ -11,7 +11,7 @@ export function parseSmallFasta(text) {
         const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
         const [id, ...descriptionLines] = defLine.split(' ');
         const description = descriptionLines.join(' ');
-        const sequence = seqLines.join('').replace(/\s/g, '');
+        const sequence = seqLines.join('').replaceAll(/\s/g, '');
         return { id, description, sequence };
     });
 }

package/esm/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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package/esm/CramAdapter/configSchema.d.ts

@@ -1,2 +1,41 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/HtsgetBamAdapter/configSchema.d.ts

@@ -1,2 +1,27 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    htsgetBase: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    htsgetTrackId: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HtsgetBamAdapter;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof AlignmentsDisplay;
 export default _default;

package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -4,4 +4,42 @@ import PluginManager from '@jbrowse/core/PluginManager';
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/LinearAlignmentsDisplay/models/model.d.ts

@@ -3,6 +3,7 @@ import { Instance, IStateTreeNode } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { MenuItem } from '@jbrowse/core/ui';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 /**
  * #stateModel LinearAlignmentsDisplay
  * extends `BaseDisplay`
@@ -16,13 +17,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
     snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
@@ -32,6 +34,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -39,6 +42,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -51,6 +55,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined; /**
+             * #property
+             * refers to LinearPileupDisplay sub-display model
+             */
         } & IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -58,17 +66,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any;
+    readonly adapterConfig: any; /**
+     * #stateModel LinearAlignmentsDisplay
+     * extends `BaseDisplay`
+     */
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -88,6 +101,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      * #getter
      */
     readonly height: any;
+    readonly featureIdUnderMouse: any;
 } & {
     /**
      * #getter
@@ -125,7 +139,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    updateStatsLimit(stats?: unknown): void;
+    setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
     /**
      * #action
      */
@@ -149,7 +163,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
-    }): Promise<JSX.Element>;
+    }): Promise<React.JSX.Element>;
 } & {
     /**
      * #method
@@ -164,7 +178,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
     snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;

package/esm/LinearAlignmentsDisplay/models/model.js

@@ -113,6 +113,10 @@ function stateModelFactory(pluginManager, configSchema) {
             var _a;
             return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
         },
+        get featureIdUnderMouse() {
+            return (self.PileupDisplay.featureIdUnderMouse ||
+                self.SNPCoverageDisplay.featureIdUnderMouse);
+        },
     }))
         .views(self => ({
         /**
@@ -182,9 +186,9 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #action
          */
-        updateStatsLimit(stats) {
-            self.PileupDisplay.updateStatsLimit(stats);
-            self.SNPCoverageDisplay.updateStatsLimit(stats);
+        setFeatureDensityStatsLimit(stats) {
+            self.PileupDisplay.setFeatureDensityStatsLimit(stats);
+            self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
         },
         /**
          * #action
@@ -249,7 +253,8 @@ function stateModelFactory(pluginManager, configSchema) {
          */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
-            await when(() => self.PileupDisplay.ready);
+            await when(() => !self.PileupDisplay.renderProps().notReady &&
+                !self.SNPCoverageDisplay.renderProps().notReady);
             return (React.createElement(React.Fragment, null,
                 React.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
                 React.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({

package/esm/LinearAlignmentsDisplay/models/model.js.map

@@ -1 +1 @@
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