@jbrowse/plugin-alignments 3.0.1 → 3.0.3

package/dist/BamAdapter/BamAdapter.d.ts

@@ -26,6 +26,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
+    setupPre2(opts?: BaseOptions): Promise<Header>;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private seqFetch;

package/dist/BamAdapter/BamAdapter.js

@@ -56,26 +56,23 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { bam } = await this.configure();
         return bam.getHeaderText();
     }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts || {};
+    async setupPre(_opts) {
         const { bam } = await this.configure();
-        this.samHeader = await (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
-            const samHeader = await bam.getHeader();
-            const idToName = [];
-            const nameToId = {};
-            samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-                const SN = sqLine.data.find(item => item.tag === 'SN');
-                if (SN) {
-                    const refName = SN.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
-            });
-            return { idToName, nameToId };
+        const samHeader = await bam.getHeader();
+        const idToName = [];
+        const nameToId = {};
+        samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
+            const SN = sqLine.data.find(item => item.tag === 'SN');
+            if (SN) {
+                const refName = SN.value;
+                nameToId[refName] = refId;
+                idToName[refId] = refName;
+            }
         });
+        this.samHeader = { idToName, nameToId };
         return this.samHeader;
     }
-    async setup(opts) {
+    async setupPre2(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
@@ -84,6 +81,10 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.setupP;
     }
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.setupPre2(opts));
+    }
     async getRefNames(opts) {
         const { idToName } = await this.setup(opts);
         return idToName;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -28,7 +28,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
-    private setup;
+    private setupPre2;
+    setup(opts?: BaseOptions): Promise<{
+        samHeader: Header;
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refNameToId(refName: string): number | undefined;
     refIdToName(refId: number): string | undefined;

package/dist/CramAdapter/CramAdapter.js

@@ -94,36 +94,33 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return sequence;
     }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
-            const conf = await this.configure();
-            const { cram } = conf;
-            const samHeader = await cram.cram.getSamHeader();
-            const idToName = [];
-            const nameToId = {};
-            samHeader
-                .filter(l => l.tag === 'SQ')
-                .forEach((sqLine, refId) => {
-                const SN = sqLine.data.find(item => item.tag === 'SN');
-                if (SN) {
-                    const refName = SN.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,
-            };
+    async setupPre(_opts) {
+        const conf = await this.configure();
+        const { cram } = conf;
+        const samHeader = await cram.cram.getSamHeader();
+        const idToName = [];
+        const nameToId = {};
+        samHeader
+            .filter(l => l.tag === 'SQ')
+            .forEach((sqLine, refId) => {
+            const SN = sqLine.data.find(item => item.tag === 'SN');
+            if (SN) {
+                const refName = SN.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,
+        };
     }
-    async setup(opts) {
+    async setupPre2(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
@@ -132,6 +129,10 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.setupP;
     }
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.setupPre2(opts));
+    }
     async getRefNames(opts) {
         const { samHeader } = await this.setup(opts);
         if (!samHeader.idToName) {

package/dist/LinearPileupDisplay/doAfterAttach.d.ts

@@ -0,0 +1,20 @@
+import type { ModificationType, SortedBy } from '../shared/types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function doAfterAttach(model: {
+    autorunReady: boolean;
+    sortedBy?: SortedBy;
+    adapterConfig: AnyConfigurationModel;
+    rendererType: {
+        name: string;
+    };
+    sortReady: boolean;
+    currSortBpPerPx: number;
+    parentTrack: any;
+    renderPropsPre: () => Record<string, unknown>;
+    setCurrSortBpPerPx: (arg: number) => void;
+    setError: (arg: unknown) => void;
+    updateVisibleModifications: (arg: ModificationType[]) => void;
+    setModificationsReady: (arg: boolean) => void;
+    setSortReady: (arg: boolean) => void;
+    setMessage: (arg: string) => void;
+}): void;

package/dist/LinearPileupDisplay/doAfterAttach.js

@@ -0,0 +1,69 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doAfterAttach = doAfterAttach;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const getUniqueModifications_1 = require("../shared/getUniqueModifications");
+const util_2 = require("../util");
+function doAfterAttach(model) {
+    (0, util_2.createAutorun)(model, async () => {
+        const view = (0, util_1.getContainingView)(model);
+        if (!model.autorunReady) {
+            return;
+        }
+        model.setCurrSortBpPerPx(view.bpPerPx);
+    }, { delay: 1000 });
+    (0, util_2.createAutorun)(model, async () => {
+        const { rpcManager } = (0, util_1.getSession)(model);
+        const view = (0, util_1.getContainingView)(model);
+        if (!model.autorunReady) {
+            return;
+        }
+        const { sortedBy, adapterConfig, rendererType, sortReady } = model;
+        const { bpPerPx } = view;
+        if (sortedBy && (!sortReady || model.currSortBpPerPx === view.bpPerPx)) {
+            const { pos, refName, assemblyName } = sortedBy;
+            await model.rendererType.renderInClient(rpcManager, {
+                assemblyName,
+                regions: [
+                    {
+                        start: pos,
+                        end: pos + 1,
+                        refName,
+                        assemblyName,
+                    },
+                ],
+                adapterConfig,
+                rendererType: rendererType.name,
+                sessionId: (0, tracks_1.getRpcSessionId)(model),
+                layoutId: view.id,
+                timeout: 1000000,
+                statusCallback: (arg) => {
+                    model.setMessage(arg);
+                },
+                ...model.renderPropsPre(),
+            });
+        }
+        if ((0, mobx_state_tree_1.isAlive)(model)) {
+            model.setCurrSortBpPerPx(bpPerPx);
+            model.setSortReady(true);
+        }
+    }, { delay: 1000 });
+    (0, util_2.createAutorun)(model, async () => {
+        if (!model.autorunReady) {
+            return;
+        }
+        const { adapterConfig } = model;
+        const { staticBlocks } = (0, util_1.getContainingView)(model);
+        const vals = await (0, getUniqueModifications_1.getUniqueModifications)({
+            model,
+            adapterConfig,
+            blocks: staticBlocks,
+        });
+        if ((0, mobx_state_tree_1.isAlive)(model)) {
+            model.updateVisibleModifications(vals);
+            model.setModificationsReady(true);
+        }
+    }, { delay: 1000 });
+}

package/dist/LinearPileupDisplay/model.js

@@ -39,7 +39,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const ColorLens_1 = __importDefault(require("@mui/icons-material/ColorLens"));
 const SwapVert_1 = __importDefault(require("@mui/icons-material/SwapVert"));
 const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
@@ -47,7 +46,6 @@ const Workspaces_1 = __importDefault(require("@mui/icons-material/Workspaces"));
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
-const getUniqueModifications_1 = require("../shared/getUniqueModifications");
 const util_2 = require("../util");
 const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTagDialog'))));
 const GroupByDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/GroupByDialog'))));
@@ -349,62 +347,17 @@ function stateModelFactory(configSchema) {
     })
         .actions(self => ({
         afterAttach() {
-            (0, util_2.createAutorun)(self, async () => {
-                const view = (0, util_1.getContainingView)(self);
-                if (!self.autorunReady) {
-                    return;
+            ;
+            (async () => {
+                try {
+                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('./doAfterAttach')));
+                    doAfterAttach(self);
                 }
-                self.setCurrSortBpPerPx(view.bpPerPx);
-            }, { delay: 1000 });
-            (0, util_2.createAutorun)(self, async () => {
-                const { rpcManager } = (0, util_1.getSession)(self);
-                const view = (0, util_1.getContainingView)(self);
-                if (!self.autorunReady) {
-                    return;
+                catch (e) {
+                    (0, util_1.getSession)(self).notifyError(`${e}`, e);
+                    console.error(e);
                 }
-                const { sortedBy, adapterConfig, rendererType, sortReady } = self;
-                const { bpPerPx } = view;
-                if (sortedBy &&
-                    (!sortReady || self.currSortBpPerPx === view.bpPerPx)) {
-                    const { pos, refName, assemblyName } = sortedBy;
-                    await self.rendererType.renderInClient(rpcManager, {
-                        assemblyName,
-                        regions: [
-                            {
-                                start: pos,
-                                end: pos + 1,
-                                refName,
-                                assemblyName,
-                            },
-                        ],
-                        adapterConfig,
-                        rendererType: rendererType.name,
-                        sessionId: (0, tracks_1.getRpcSessionId)(self),
-                        layoutId: view.id,
-                        timeout: 1000000,
-                        ...self.renderPropsPre(),
-                    });
-                }
-                if ((0, mobx_state_tree_1.isAlive)(self)) {
-                    self.setCurrSortBpPerPx(bpPerPx);
-                    self.setSortReady(true);
-                }
-            }, { delay: 1000 });
-            (0, util_2.createAutorun)(self, async () => {
-                if (!self.autorunReady) {
-                    return;
-                }
-                const { staticBlocks } = (0, util_1.getContainingView)(self);
-                const vals = await (0, getUniqueModifications_1.getUniqueModifications)({
-                    self,
-                    adapterConfig: (0, configuration_1.getConf)(self.parentTrack, 'adapter'),
-                    blocks: staticBlocks,
-                });
-                if ((0, mobx_state_tree_1.isAlive)(self)) {
-                    self.updateVisibleModifications(vals);
-                    self.setModificationsReady(true);
-                }
-            });
+            })();
         },
     }));
 }

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -97,6 +97,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
+    invertedSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
     showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;

package/dist/LinearSNPCoverageDisplay/model.js

@@ -171,7 +171,7 @@ function stateModelFactory(pluginManager, configSchema) {
                 const { colorBy } = self;
                 if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
                     const vals = await (0, getUniqueModifications_1.getUniqueModifications)({
-                        self,
+                        model: self,
                         adapterConfig: (0, configuration_1.getConf)(self.parentTrack, 'adapter'),
                         blocks: staticBlocks,
                     });
@@ -218,7 +218,7 @@ function stateModelFactory(pluginManager, configSchema) {
             get rendererTypeName() {
                 return rendererTypes.get('snpcoverage');
             },
-            get needsScalebar() {
+            get graphType() {
                 return true;
             },
             contextMenuItems() {
@@ -242,7 +242,7 @@ function stateModelFactory(pluginManager, configSchema) {
                         type: 'checkbox',
                         checked: self.showInterbaseCountsSetting,
                         onClick: () => {
-                            self.setShowInterbaseCounts(self.showInterbaseCountsSetting);
+                            self.setShowInterbaseCounts(!self.showInterbaseCountsSetting);
                         },
                     },
                     {
@@ -251,7 +251,7 @@ function stateModelFactory(pluginManager, configSchema) {
                         type: 'checkbox',
                         checked: self.showArcsSetting,
                         onClick: () => {
-                            self.setShowArcs(self.showArcsSetting);
+                            self.setShowArcs(!self.showArcsSetting);
                         },
                     },
                 ];

package/dist/PileupRPC/methods/GetGlobalValueForTag.js

@@ -13,9 +13,10 @@ class PileupGetGlobalValueForTag extends base_1.default {
         this.name = 'PileupGetGlobalValueForTag';
     }
     async execute(args, rpcDriver) {
-        const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
         const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions, deserializedArgs);
         const featuresArray = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
         return [
             ...new Set(featuresArray

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -16,10 +16,12 @@ class PileupGetReducedFeatures extends base_1.default {
         this.name = 'PileupGetReducedFeatures';
     }
     async execute(args, rpcDriver) {
-        const des = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = des;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions } = deserializedArgs;
         const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe((0, operators_1.toArray)()));
+        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe((0, operators_1.toArray)()));
         const reduced = (0, util_1.dedupe)(featuresArray.map(f => {
             var _a;
             return ({

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -15,17 +15,20 @@ class PileupGetVisibleModifications extends base_1.default {
         this.name = 'PileupGetVisibleModifications';
     }
     async execute(args, rpcDriver) {
-        const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
+        const deserializeArguments = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions } = deserializeArguments;
         const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions).pipe((0, operators_1.toArray)()));
+        const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializeArguments)
+            .pipe((0, operators_1.toArray)()));
         const uniqueModifications = new Map();
-        featuresArray.forEach(f => {
-            for (const mod of (0, ModificationParser_1.getModTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '')) {
+        for (const feat of featuresArray) {
+            for (const mod of (0, ModificationParser_1.getModTypes)((0, util_1.getTagAlt)(feat, 'MM', 'Mm') || '')) {
                 if (!uniqueModifications.has(mod.type)) {
                     uniqueModifications.set(mod.type, mod);
                 }
             }
-        });
+        }
         return [...uniqueModifications.values()];
     }
 }

package/dist/PileupRenderer/PileupRenderer.js

@@ -75,31 +75,33 @@ class PileupRenderer extends BoxRendererType_1.default {
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
-        const { colorBy, regions, bpPerPx } = renderProps;
+        const { statusCallback = () => { }, colorBy, regions, bpPerPx } = renderProps;
         const region = regions[0];
-        const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
-            ? await this.fetchSequence(renderProps, region)
-            : undefined;
-        const { layoutRecords, height } = (0, layoutFeatures_1.layoutFeats)({
+        const width = (region.end - region.start) / bpPerPx;
+        const { layoutRecords, height } = await (0, util_1.updateStatus)('Creating layout', statusCallback, () => (0, layoutFeatures_1.layoutFeats)({
             ...renderProps,
             features,
             layout,
-        });
-        const width = (region.end - region.start) / bpPerPx;
-        const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
-        const res = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
-            makeImageData({
-                ctx,
-                layoutRecords,
-                canvasWidth: width,
-                renderArgs: {
-                    ...renderProps,
-                    layout,
-                    features,
-                    regionSequence,
-                },
+        }));
+        const res = await (0, util_1.updateStatus)('Rendering alignments', statusCallback, async () => {
+            const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
+                ? await this.fetchSequence(renderProps, region)
+                : undefined;
+            const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
+            return (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
+                makeImageData({
+                    ctx,
+                    layoutRecords,
+                    canvasWidth: width,
+                    renderArgs: {
+                        ...renderProps,
+                        layout,
+                        features,
+                        regionSequence,
+                    },
+                });
+                return undefined;
             });
-            return undefined;
         });
         const results = await super.render({
             ...renderProps,

package/dist/PileupRenderer/types.d.ts

@@ -14,6 +14,7 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     sortedBy?: SortedBy;
     showSoftClip: boolean;
     highResolutionScaling: number;
+    statusCallback?: (arg: string) => void;
 }
 export interface ProcessedRenderArgs extends RenderArgsDeserialized {
     features: Map<string, Feature>;

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -33,11 +33,13 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
+const util_1 = require("@jbrowse/core/util");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
     async draw(ctx, props) {
+        const { statusCallback = () => { } } = props;
         const { makeImage } = await Promise.resolve().then(() => __importStar(require('./makeImage')));
-        await makeImage(ctx, props);
+        await (0, util_1.updateStatus)('Rendering coverage', statusCallback, () => makeImage(ctx, props));
         return undefined;
     }
 }

package/dist/SNPCoverageRenderer/types.d.ts

@@ -15,5 +15,6 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
     };
     displayCrossHatches: boolean;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
+    statusCallback?: (arg: string) => void;
     colorBy: ColorBy;
 }

package/dist/shared/getUniqueModifications.d.ts

@@ -2,13 +2,14 @@ import type { ModificationType } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BlockSet } from '@jbrowse/core/util/blockTypes';
 import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getUniqueModifications({ self, adapterConfig, blocks, opts, }: {
-    self: IAnyStateTreeNode;
+export interface ModificationOpts {
+    headers?: Record<string, string>;
+    stopToken?: string;
+    filters: string[];
+}
+export declare function getUniqueModifications({ model, adapterConfig, blocks, opts, }: {
+    model: IAnyStateTreeNode;
     adapterConfig: AnyConfigurationModel;
     blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        stopToken?: string;
-        filters: string[];
-    };
+    opts?: ModificationOpts;
 }): Promise<ModificationType[]>;

package/dist/shared/getUniqueModifications.js

@@ -3,13 +3,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getUniqueModifications = getUniqueModifications;
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-async function getUniqueModifications({ self, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
+    const { rpcManager } = (0, util_1.getSession)(model);
+    const sessionId = (0, tracks_1.getRpcSessionId)(model);
     const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
         adapterConfig,
         sessionId,
         regions: blocks.contentBlocks,
+        statusCallback: (arg) => {
+            model.setMessage(arg);
+        },
         ...opts,
     });
     return values;

package/esm/BamAdapter/BamAdapter.d.ts

@@ -26,6 +26,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
+    setupPre2(opts?: BaseOptions): Promise<Header>;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private seqFetch;

package/esm/BamAdapter/BamAdapter.js

@@ -51,26 +51,23 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         const { bam } = await this.configure();
         return bam.getHeaderText();
     }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts || {};
+    async setupPre(_opts) {
         const { bam } = await this.configure();
-        this.samHeader = await updateStatus('Downloading index', statusCallback, async () => {
-            const samHeader = await bam.getHeader();
-            const idToName = [];
-            const nameToId = {};
-            samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-                const SN = sqLine.data.find(item => item.tag === 'SN');
-                if (SN) {
-                    const refName = SN.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
-            });
-            return { idToName, nameToId };
+        const samHeader = await bam.getHeader();
+        const idToName = [];
+        const nameToId = {};
+        samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
+            const SN = sqLine.data.find(item => item.tag === 'SN');
+            if (SN) {
+                const refName = SN.value;
+                nameToId[refName] = refId;
+                idToName[refId] = refName;
+            }
         });
+        this.samHeader = { idToName, nameToId };
         return this.samHeader;
     }
-    async setup(opts) {
+    async setupPre2(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
@@ -79,6 +76,10 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         }
         return this.setupP;
     }
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.setupPre2(opts));
+    }
     async getRefNames(opts) {
         const { idToName } = await this.setup(opts);
         return idToName;

package/esm/CramAdapter/CramAdapter.d.ts

@@ -28,7 +28,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
-    private setup;
+    private setupPre2;
+    setup(opts?: BaseOptions): Promise<{
+        samHeader: Header;
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refNameToId(refName: string): number | undefined;
     refIdToName(refId: number): string | undefined;

package/esm/CramAdapter/CramAdapter.js

@@ -89,36 +89,33 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         return sequence;
     }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return updateStatus('Downloading index', statusCallback, async () => {
-            const conf = await this.configure();
-            const { cram } = conf;
-            const samHeader = await cram.cram.getSamHeader();
-            const idToName = [];
-            const nameToId = {};
-            samHeader
-                .filter(l => l.tag === 'SQ')
-                .forEach((sqLine, refId) => {
-                const SN = sqLine.data.find(item => item.tag === 'SN');
-                if (SN) {
-                    const refName = SN.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,
-            };
+    async setupPre(_opts) {
+        const conf = await this.configure();
+        const { cram } = conf;
+        const samHeader = await cram.cram.getSamHeader();
+        const idToName = [];
+        const nameToId = {};
+        samHeader
+            .filter(l => l.tag === 'SQ')
+            .forEach((sqLine, refId) => {
+            const SN = sqLine.data.find(item => item.tag === 'SN');
+            if (SN) {
+                const refName = SN.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,
+        };
     }
-    async setup(opts) {
+    async setupPre2(opts) {
         if (!this.setupP) {
             this.setupP = this.setupPre(opts).catch((e) => {
                 this.setupP = undefined;
@@ -127,6 +124,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         return this.setupP;
     }
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.setupPre2(opts));
+    }
     async getRefNames(opts) {
         const { samHeader } = await this.setup(opts);
         if (!samHeader.idToName) {

package/esm/LinearPileupDisplay/doAfterAttach.d.ts

@@ -0,0 +1,20 @@
+import type { ModificationType, SortedBy } from '../shared/types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function doAfterAttach(model: {
+    autorunReady: boolean;
+    sortedBy?: SortedBy;
+    adapterConfig: AnyConfigurationModel;
+    rendererType: {
+        name: string;
+    };
+    sortReady: boolean;
+    currSortBpPerPx: number;
+    parentTrack: any;
+    renderPropsPre: () => Record<string, unknown>;
+    setCurrSortBpPerPx: (arg: number) => void;
+    setError: (arg: unknown) => void;
+    updateVisibleModifications: (arg: ModificationType[]) => void;
+    setModificationsReady: (arg: boolean) => void;
+    setSortReady: (arg: boolean) => void;
+    setMessage: (arg: string) => void;
+}): void;

package/esm/LinearPileupDisplay/doAfterAttach.js

@@ -0,0 +1,66 @@
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { isAlive } from 'mobx-state-tree';
+import { getUniqueModifications } from '../shared/getUniqueModifications';
+import { createAutorun } from '../util';
+export function doAfterAttach(model) {
+    createAutorun(model, async () => {
+        const view = getContainingView(model);
+        if (!model.autorunReady) {
+            return;
+        }
+        model.setCurrSortBpPerPx(view.bpPerPx);
+    }, { delay: 1000 });
+    createAutorun(model, async () => {
+        const { rpcManager } = getSession(model);
+        const view = getContainingView(model);
+        if (!model.autorunReady) {
+            return;
+        }
+        const { sortedBy, adapterConfig, rendererType, sortReady } = model;
+        const { bpPerPx } = view;
+        if (sortedBy && (!sortReady || model.currSortBpPerPx === view.bpPerPx)) {
+            const { pos, refName, assemblyName } = sortedBy;
+            await model.rendererType.renderInClient(rpcManager, {
+                assemblyName,
+                regions: [
+                    {
+                        start: pos,
+                        end: pos + 1,
+                        refName,
+                        assemblyName,
+                    },
+                ],
+                adapterConfig,
+                rendererType: rendererType.name,
+                sessionId: getRpcSessionId(model),
+                layoutId: view.id,
+                timeout: 1000000,
+                statusCallback: (arg) => {
+                    model.setMessage(arg);
+                },
+                ...model.renderPropsPre(),
+            });
+        }
+        if (isAlive(model)) {
+            model.setCurrSortBpPerPx(bpPerPx);
+            model.setSortReady(true);
+        }
+    }, { delay: 1000 });
+    createAutorun(model, async () => {
+        if (!model.autorunReady) {
+            return;
+        }
+        const { adapterConfig } = model;
+        const { staticBlocks } = getContainingView(model);
+        const vals = await getUniqueModifications({
+            model,
+            adapterConfig,
+            blocks: staticBlocks,
+        });
+        if (isAlive(model)) {
+            model.updateVisibleModifications(vals);
+            model.setModificationsReady(true);
+        }
+    }, { delay: 1000 });
+}

package/esm/LinearPileupDisplay/model.js

@@ -1,16 +1,14 @@
 import { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { getContainingView, getEnv, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import ColorLensIcon from '@mui/icons-material/ColorLens';
 import SwapVertIcon from '@mui/icons-material/SwapVert';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import WorkspacesIcon from '@mui/icons-material/Workspaces';
 import { observable } from 'mobx';
-import { isAlive, types } from 'mobx-state-tree';
+import { types } from 'mobx-state-tree';
 import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
-import { getUniqueModifications } from '../shared/getUniqueModifications';
-import { createAutorun, getColorForModification, modificationData, } from '../util';
+import { getColorForModification, modificationData } from '../util';
 const SortByTagDialog = lazy(() => import('./components/SortByTagDialog'));
 const GroupByDialog = lazy(() => import('./components/GroupByDialog'));
 function stateModelFactory(configSchema) {
@@ -311,62 +309,17 @@ function stateModelFactory(configSchema) {
     })
         .actions(self => ({
         afterAttach() {
-            createAutorun(self, async () => {
-                const view = getContainingView(self);
-                if (!self.autorunReady) {
-                    return;
+            ;
+            (async () => {
+                try {
+                    const { doAfterAttach } = await import('./doAfterAttach');
+                    doAfterAttach(self);
                 }
-                self.setCurrSortBpPerPx(view.bpPerPx);
-            }, { delay: 1000 });
-            createAutorun(self, async () => {
-                const { rpcManager } = getSession(self);
-                const view = getContainingView(self);
-                if (!self.autorunReady) {
-                    return;
+                catch (e) {
+                    getSession(self).notifyError(`${e}`, e);
+                    console.error(e);
                 }
-                const { sortedBy, adapterConfig, rendererType, sortReady } = self;
-                const { bpPerPx } = view;
-                if (sortedBy &&
-                    (!sortReady || self.currSortBpPerPx === view.bpPerPx)) {
-                    const { pos, refName, assemblyName } = sortedBy;
-                    await self.rendererType.renderInClient(rpcManager, {
-                        assemblyName,
-                        regions: [
-                            {
-                                start: pos,
-                                end: pos + 1,
-                                refName,
-                                assemblyName,
-                            },
-                        ],
-                        adapterConfig,
-                        rendererType: rendererType.name,
-                        sessionId: getRpcSessionId(self),
-                        layoutId: view.id,
-                        timeout: 1000000,
-                        ...self.renderPropsPre(),
-                    });
-                }
-                if (isAlive(self)) {
-                    self.setCurrSortBpPerPx(bpPerPx);
-                    self.setSortReady(true);
-                }
-            }, { delay: 1000 });
-            createAutorun(self, async () => {
-                if (!self.autorunReady) {
-                    return;
-                }
-                const { staticBlocks } = getContainingView(self);
-                const vals = await getUniqueModifications({
-                    self,
-                    adapterConfig: getConf(self.parentTrack, 'adapter'),
-                    blocks: staticBlocks,
-                });
-                if (isAlive(self)) {
-                    self.updateVisibleModifications(vals);
-                    self.setModificationsReady(true);
-                }
-            });
+            })();
         },
     }));
 }

package/esm/LinearSNPCoverageDisplay/model.d.ts

@@ -97,6 +97,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
+    invertedSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
     showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;

package/esm/LinearSNPCoverageDisplay/model.js

@@ -133,7 +133,7 @@ function stateModelFactory(pluginManager, configSchema) {
                 const { colorBy } = self;
                 if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
                     const vals = await getUniqueModifications({
-                        self,
+                        model: self,
                         adapterConfig: getConf(self.parentTrack, 'adapter'),
                         blocks: staticBlocks,
                     });
@@ -180,7 +180,7 @@ function stateModelFactory(pluginManager, configSchema) {
             get rendererTypeName() {
                 return rendererTypes.get('snpcoverage');
             },
-            get needsScalebar() {
+            get graphType() {
                 return true;
             },
             contextMenuItems() {
@@ -204,7 +204,7 @@ function stateModelFactory(pluginManager, configSchema) {
                         type: 'checkbox',
                         checked: self.showInterbaseCountsSetting,
                         onClick: () => {
-                            self.setShowInterbaseCounts(self.showInterbaseCountsSetting);
+                            self.setShowInterbaseCounts(!self.showInterbaseCountsSetting);
                         },
                     },
                     {
@@ -213,7 +213,7 @@ function stateModelFactory(pluginManager, configSchema) {
                         type: 'checkbox',
                         checked: self.showArcsSetting,
                         onClick: () => {
-                            self.setShowArcs(self.showArcsSetting);
+                            self.setShowArcs(!self.showArcsSetting);
                         },
                     },
                 ];

package/esm/PileupRPC/methods/GetGlobalValueForTag.js

@@ -8,9 +8,10 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
         this.name = 'PileupGetGlobalValueForTag';
     }
     async execute(args, rpcDriver) {
-        const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions, deserializedArgs);
         const featuresArray = await firstValueFrom(features.pipe(toArray()));
         return [
             ...new Set(featuresArray

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -11,10 +11,12 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
         this.name = 'PileupGetReducedFeatures';
     }
     async execute(args, rpcDriver) {
-        const des = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = des;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions } = deserializedArgs;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe(toArray()));
+        const featuresArray = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe(toArray()));
         const reduced = dedupe(featuresArray.map(f => {
             var _a;
             return ({

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -10,17 +10,20 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
         this.name = 'PileupGetVisibleModifications';
     }
     async execute(args, rpcDriver) {
-        const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
+        const deserializeArguments = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions } = deserializeArguments;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions).pipe(toArray()));
+        const featuresArray = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializeArguments)
+            .pipe(toArray()));
         const uniqueModifications = new Map();
-        featuresArray.forEach(f => {
-            for (const mod of getModTypes(getTagAlt(f, 'MM', 'Mm') || '')) {
+        for (const feat of featuresArray) {
+            for (const mod of getModTypes(getTagAlt(feat, 'MM', 'Mm') || '')) {
                 if (!uniqueModifications.has(mod.type)) {
                     uniqueModifications.set(mod.type, mod);
                 }
             }
-        });
+        }
         return [...uniqueModifications.values()];
     }
 }

package/esm/PileupRenderer/PileupRenderer.js

@@ -1,7 +1,7 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { renderToAbstractCanvas } from '@jbrowse/core/util';
+import { renderToAbstractCanvas, updateStatus } from '@jbrowse/core/util';
 import { PileupLayoutSession } from './PileupLayoutSession';
 import { fetchSequence } from '../util';
 import { layoutFeats } from './layoutFeatures';
@@ -37,31 +37,33 @@ export default class PileupRenderer extends BoxRendererType {
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
-        const { colorBy, regions, bpPerPx } = renderProps;
+        const { statusCallback = () => { }, colorBy, regions, bpPerPx } = renderProps;
         const region = regions[0];
-        const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
-            ? await this.fetchSequence(renderProps, region)
-            : undefined;
-        const { layoutRecords, height } = layoutFeats({
+        const width = (region.end - region.start) / bpPerPx;
+        const { layoutRecords, height } = await updateStatus('Creating layout', statusCallback, () => layoutFeats({
             ...renderProps,
             features,
             layout,
-        });
-        const width = (region.end - region.start) / bpPerPx;
-        const { makeImageData } = await import('./makeImageData');
-        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
-            makeImageData({
-                ctx,
-                layoutRecords,
-                canvasWidth: width,
-                renderArgs: {
-                    ...renderProps,
-                    layout,
-                    features,
-                    regionSequence,
-                },
+        }));
+        const res = await updateStatus('Rendering alignments', statusCallback, async () => {
+            const regionSequence = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' && features.size
+                ? await this.fetchSequence(renderProps, region)
+                : undefined;
+            const { makeImageData } = await import('./makeImageData');
+            return renderToAbstractCanvas(width, height, renderProps, ctx => {
+                makeImageData({
+                    ctx,
+                    layoutRecords,
+                    canvasWidth: width,
+                    renderArgs: {
+                        ...renderProps,
+                        layout,
+                        features,
+                        regionSequence,
+                    },
+                });
+                return undefined;
             });
-            return undefined;
         });
         const results = await super.render({
             ...renderProps,

package/esm/PileupRenderer/types.d.ts

@@ -14,6 +14,7 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     sortedBy?: SortedBy;
     showSoftClip: boolean;
     highResolutionScaling: number;
+    statusCallback?: (arg: string) => void;
 }
 export interface ProcessedRenderArgs extends RenderArgsDeserialized {
     features: Map<string, Feature>;

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,8 +1,10 @@
+import { updateStatus } from '@jbrowse/core/util';
 import { WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     async draw(ctx, props) {
+        const { statusCallback = () => { } } = props;
         const { makeImage } = await import('./makeImage');
-        await makeImage(ctx, props);
+        await updateStatus('Rendering coverage', statusCallback, () => makeImage(ctx, props));
         return undefined;
     }
 }

package/esm/SNPCoverageRenderer/types.d.ts

@@ -15,5 +15,6 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
     };
     displayCrossHatches: boolean;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
+    statusCallback?: (arg: string) => void;
     colorBy: ColorBy;
 }

package/esm/shared/getUniqueModifications.d.ts

@@ -2,13 +2,14 @@ import type { ModificationType } from './types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BlockSet } from '@jbrowse/core/util/blockTypes';
 import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getUniqueModifications({ self, adapterConfig, blocks, opts, }: {
-    self: IAnyStateTreeNode;
+export interface ModificationOpts {
+    headers?: Record<string, string>;
+    stopToken?: string;
+    filters: string[];
+}
+export declare function getUniqueModifications({ model, adapterConfig, blocks, opts, }: {
+    model: IAnyStateTreeNode;
     adapterConfig: AnyConfigurationModel;
     blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        stopToken?: string;
-        filters: string[];
-    };
+    opts?: ModificationOpts;
 }): Promise<ModificationType[]>;

package/esm/shared/getUniqueModifications.js

@@ -1,12 +1,15 @@
 import { getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-export async function getUniqueModifications({ self, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = getSession(self);
-    const sessionId = getRpcSessionId(self);
+export async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
+    const { rpcManager } = getSession(model);
+    const sessionId = getRpcSessionId(model);
     const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
         adapterConfig,
         sessionId,
         regions: blocks.contentBlocks,
+        statusCallback: (arg) => {
+            model.setMessage(arg);
+        },
         ...opts,
     });
     return values;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.0.1",
+  "version": "3.0.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^5.0.0",
     "@gmod/cram": "^4.0.1",
-    "@jbrowse/core": "^3.0.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
-    "@jbrowse/plugin-wiggle": "^3.0.1",
-    "@jbrowse/sv-core": "^3.0.1",
+    "@jbrowse/core": "^3.0.3",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.3",
+    "@jbrowse/plugin-wiggle": "^3.0.3",
+    "@jbrowse/sv-core": "^3.0.3",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
+  "gitHead": "f516540428282351d26e46743e69a724651bfb2c"
 }