@jbrowse/plugin-alignments 2.6.2 → 2.7.0

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-declare const _default: (props: {
+declare const AlignmentsFeatureDetails: (props: {
     model: IAnyStateTreeNode;
 }) => React.JSX.Element;
-export default _default;
+export default AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -120,7 +120,7 @@ function PairLink({ locString, model, }) {
             (0, util_1.navToLoc)(locString, model);
         }, href: "#" }, locString));
 }
-exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(props) {
+const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const feat = (0, clone_1.default)(model.featureData);
     const SA = (0, util_1.getTag)('SA', feat);
@@ -131,3 +131,4 @@ exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(pr
         SA ? react_1.default.createElement(AlignmentsFeatureSuppAligns_1.default, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (react_1.default.createElement(AlignmentsFeatureFlags_1.default, { feature: feat, ...props })) : null));
 });
+exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -1,8 +1,6 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
-    tags?: {
-        [key: string]: unknown;
-    };
+    tags?: Record<string, unknown>;
     [key: string]: unknown;
 }): unknown;
 export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -2,6 +2,7 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
+import { IFilter } from '../shared';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -29,15 +30,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: {
-            flagInclude: number;
-            flagExclude: number;
-            tagFilter: {
-                tag: string;
-                value: unknown;
-            };
-            readName: string;
-        };
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -2,20 +2,12 @@ import { IndexedCramFile, CramRecord } from '@gmod/cram';
 import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+import { IFilter } from '../shared';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
     readGroups?: (string | undefined)[];
 }
-interface FilterBy {
-    flagInclude: number;
-    flagExclude: number;
-    tagFilter: {
-        tag: string;
-        value: unknown;
-    };
-    readName: string;
-}
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
@@ -30,7 +22,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         cram: IndexedCramFile;
         sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -41,7 +33,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: FilterBy;
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;

package/dist/CramAdapter/CramAdapter.js

@@ -10,6 +10,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
 const rxjs_2 = require("rxjs");
+// locals
 const CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
 class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -54,7 +55,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.configureP;
     }
-    async getHeader(opts) {
+    async getHeader(_opts) {
         const { cram } = await this.configure();
         return cram.cram.getHeaderText();
     }

package/dist/CramAdapter/util.js

@@ -11,9 +11,7 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
     let refPos = 0;
     let sublen = 0;
     let lastPos = start;
-    for (let i = 0; i < readFeatures.length; i++) {
-        const f = readFeatures[i];
-        const { code, pos, data, sub, ref } = f;
+    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
         sublen = refPos - lastPos;
         lastPos = refPos;
         if (sublen && insLen > 0) {
@@ -25,7 +23,7 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
             insLen = 0;
         }
-        refPos = f.refPos - 1 - start;
+        refPos = p - 1 - start;
         if (code === 'X') {
             // substitution
             mismatches[j++] = {
@@ -134,8 +132,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     let sublen = 0;
     let insLen = 0;
     if (readFeatures !== undefined) {
-        for (let i = 0; i < readFeatures.length; i++) {
-            const { code, refPos, sub, data } = readFeatures[i];
+        for (const { code, refPos, sub, data } of readFeatures) {
             sublen = refPos - lastPos;
             seq += ref.slice(lastPos - refStart, refPos - refStart);
             lastPos = refPos;

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

@@ -1,7 +1,6 @@
 import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
-declare function AlignmentsDisplay({ model }: {
+declare const AlignmentsDisplay: ({ model, }: {
     model: AlignmentsDisplayModel;
-}): React.JSX.Element | null;
-declare const _default: typeof AlignmentsDisplay;
-export default _default;
+}) => React.JSX.Element | null;
+export default AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -15,7 +15,7 @@ const useStyles = (0, mui_1.makeStyles)()({
         zIndex: 2,
     },
 });
-function AlignmentsDisplay({ model }) {
+const AlignmentsDisplay = (0, mobx_react_1.observer)(function AlignmentsDisplay({ model, }) {
     var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
@@ -35,5 +35,5 @@ function AlignmentsDisplay({ model }) {
                 top,
             } },
             react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
-}
-exports.default = (0, mobx_react_1.observer)(AlignmentsDisplay);
+});
+exports.default = AlignmentsDisplay;

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

@@ -55,10 +55,7 @@ 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
-             */
+            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>;
@@ -69,14 +66,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any; /**
-     * #stateModel LinearAlignmentsDisplay
-     * extends `BaseDisplay`
-     */
+    readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: React.FC<any> | undefined; /**
+     * #action
+     */
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): null;

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable react-refresh/only-export-components */
 const react_1 = __importDefault(require("react"));
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");