@jbrowse/plugin-alignments 2.11.0 → 2.11.2

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/dist/BamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'BamAdapter',
@@ -37,4 +37,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = BamAdapterF;

package/dist/CramAdapter/CramTestAdapters.js

@@ -64,6 +64,7 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new simpleFeature_1.default({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/dist/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/dist/CramAdapter/index.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'CramAdapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = CramAdapterF;

package/dist/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/dist/GuessAlignmentsTypes/index.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -52,4 +52,5 @@ exports.default = (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}
+exports.default = GuessAlignmentsTypesF;

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/dist/HtsgetBamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-exports.default = (pluginManager) => {
+function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'HtsgetBamAdapter',
@@ -40,4 +40,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = HtsgetBamAdapterF;

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/dist/LinearAlignmentsDisplay/index.js

@@ -8,7 +8,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
 const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
-function default_1(pluginManager) {
+function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -22,4 +22,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = LinearAlignmentsDisplayF;

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

@@ -25,7 +25,9 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         type: string;
         description: string;
         defaultValue: number;
-    };
+    }; /**
+     * #slot
+     */
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
@@ -42,4 +44,9 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -97,6 +97,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -247,22 +252,19 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
-    readonly selectedFeatureId: string | undefined; /**
-     * #action
-     */
+    readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined; /**
-     * #action
-     */
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -511,6 +513,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;

package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -36,7 +36,9 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
-        description: string;
+        description: string; /**
+         * #slot
+         */
         defaultValue: number;
     };
     fetchSizeLimit: {
@@ -48,12 +50,19 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     mouseover: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/dist/LinearPileupDisplay/model.d.ts

@@ -92,6 +92,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     configuration: AnyConfigurationSchemaType;
@@ -234,9 +239,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
-     * #getter
-     */
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -244,10 +247,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
-     * #method
-     */
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -60,5 +60,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/dist/LinearReadArcsDisplay/model.d.ts

@@ -103,9 +103,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRendered(): null;
 } & {
     setMessage(arg?: string | undefined): void;
-    setError(error?: unknown): void; /**
-     * #getter
-     */
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {

package/dist/LinearReadCloudDisplay/configSchema.d.ts

@@ -33,9 +33,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     maxFeatureScreenDensity: {
         type: string;
         description: string;
-        defaultValue: number; /**
+        /**
          * #slot
          */
+        defaultValue: number;
     };
     fetchSizeLimit: {
         type: string;
@@ -53,5 +54,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -67,9 +67,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         description: string;
     };
     height: {
-        type: string; /**
-         * #slot
-         */
+        type: string;
         defaultValue: number;
         description: string;
     };
@@ -79,4 +77,9 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

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

@@ -92,6 +92,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             description: string;
             defaultValue: string;
             contextVariable: string[];
+        }; /**
+         * #property
+         */
+        jexlFilters: {
+            type: string;
+            description: string; /**
+             * #property
+             */
+            defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {

package/dist/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/dist/PileupRPC/index.js

@@ -1,8 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const rpcMethods_1 = require("./rpcMethods");
-exports.default = (pm) => {
+function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
-};
+}
+exports.default = PileupRPCMethodsF;

package/dist/PileupRenderer/renderSoftClipping.js

@@ -3,6 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSoftClipping = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+// locals
+const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
 function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
@@ -17,19 +19,16 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
         return;
     }
     const heightLim = charHeight - 2;
-    for (const mismatch of mismatches) {
-        if (mismatch.type === 'softclip') {
-            const len = mismatch.cliplen || 0;
-            const s = feature.get('start');
-            const start = mismatch.start === 0 ? s - len : s + mismatch.start;
-            for (let k = 0; k < len; k += 1) {
-                const base = seq.charAt(k + mismatch.start);
-                // If softclip length+start is longer than sequence, no need to
-                // continue showing base
-                if (!base) {
-                    return;
-                }
-                const s0 = start + k;
+    const CIGAR = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+    let seqOffset = 0;
+    let refOffset = 0;
+    for (let i = 0; i < CIGAR.length; i += 2) {
+        const op = CIGAR[i + 1];
+        const len = +CIGAR[i];
+        if (op === 'S') {
+            for (let k = 0; k < len; k++) {
+                const base = seq[seqOffset + k];
+                const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s0, s0 + 1, region, bpPerPx);
                 const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
                 // Black accounts for IUPAC ambiguity code bases such as N that
@@ -42,6 +41,23 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
                     ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }
+            seqOffset += len;
+        }
+        if (op === 'N') {
+            refOffset += len;
+        }
+        if (op === 'M' || op === '=' || op === 'X') {
+            refOffset += len;
+            seqOffset += len;
+        }
+        if (op === 'H') {
+            // do nothing
+        }
+        if (op === 'D') {
+            refOffset += len;
+        }
+        if (op === 'I') {
+            seqOffset += len;
         }
     }
 }

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function SNPCoverageAdapterF(pluginManager: PluginManager): void;

package/dist/SNPCoverageAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-function default_1(pluginManager) {
+function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'SNPCoverageAdapter',
@@ -41,4 +41,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = SNPCoverageAdapterF;

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/esm/BamAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'BamAdapter',
@@ -9,4 +9,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./BamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/CramAdapter/CramTestAdapters.js

@@ -56,6 +56,7 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new SimpleFeature({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/esm/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/esm/CramAdapter/index.js

@@ -1,7 +1,7 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 // locals
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./CramAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/esm/GuessAlignmentsTypes/index.js

@@ -1,5 +1,5 @@
 import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -50,4 +50,4 @@ export default (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}

package/esm/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/esm/HtsgetBamAdapter/index.js

@@ -1,6 +1,6 @@
 import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-export default (pluginManager) => {
+export default function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'HtsgetBamAdapter',
@@ -12,4 +12,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/esm/LinearAlignmentsDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './models/configSchema';
 import modelFactory from './models/model';
 import ReactComponent from './components/AlignmentsDisplay';
-export default function (pluginManager) {
+export default function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({

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

@@ -25,7 +25,9 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         type: string;
         description: string;
         defaultValue: number;
-    };
+    }; /**
+     * #slot
+     */
     fetchSizeLimit: {
         type: string;
         defaultValue: number;
@@ -42,4 +44,9 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -97,6 +97,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
@@ -247,22 +252,19 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
-    readonly selectedFeatureId: string | undefined; /**
-     * #action
-     */
+    readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined; /**
-     * #action
-     */
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
+    navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
@@ -511,6 +513,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;

package/esm/LinearPileupDisplay/configSchema.d.ts

@@ -36,7 +36,9 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
-        description: string;
+        description: string; /**
+         * #slot
+         */
         defaultValue: number;
     };
     fetchSizeLimit: {
@@ -48,12 +50,19 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         type: string;
         defaultValue: number;
         description: string;
-    };
+    }; /**
+     * #slot
+     */
     mouseover: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/esm/LinearPileupDisplay/model.d.ts

@@ -92,6 +92,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     configuration: AnyConfigurationSchemaType;
@@ -234,9 +239,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
-     * #getter
-     */
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -244,10 +247,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
-     * #method
-     */
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;

package/esm/LinearReadArcsDisplay/configSchema.d.ts

@@ -60,5 +60,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -103,9 +103,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRendered(): null;
 } & {
     setMessage(arg?: string | undefined): void;
-    setError(error?: unknown): void; /**
-     * #getter
-     */
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {

package/esm/LinearReadCloudDisplay/configSchema.d.ts

@@ -33,9 +33,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
     maxFeatureScreenDensity: {
         type: string;
         description: string;
-        defaultValue: number; /**
+        /**
          * #slot
          */
+        defaultValue: number;
     };
     fetchSizeLimit: {
         type: string;
@@ -53,5 +54,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

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

@@ -67,9 +67,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         description: string;
     };
     height: {
-        type: string; /**
-         * #slot
-         */
+        type: string;
         defaultValue: number;
         description: string;
     };
@@ -79,4 +77,9 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

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

@@ -92,6 +92,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             description: string;
             defaultValue: string;
             contextVariable: string[];
+        }; /**
+         * #property
+         */
+        jexlFilters: {
+            type: string;
+            description: string; /**
+             * #property
+             */
+            defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {

package/esm/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/esm/PileupRPC/index.js

@@ -1,6 +1,6 @@
 import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, PileupGetReducedFeatures, } from './rpcMethods';
-export default (pm) => {
+export default function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new PileupGetReducedFeatures(pm));
-};
+}

package/esm/PileupRenderer/renderSoftClipping.js

@@ -1,5 +1,7 @@
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { bpSpanPx } from '@jbrowse/core/util';
+// locals
+import { parseCigar } from '../MismatchParser';
 import { fillRect, getCharWidthHeight } from './util';
 export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
@@ -14,19 +16,16 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
         return;
     }
     const heightLim = charHeight - 2;
-    for (const mismatch of mismatches) {
-        if (mismatch.type === 'softclip') {
-            const len = mismatch.cliplen || 0;
-            const s = feature.get('start');
-            const start = mismatch.start === 0 ? s - len : s + mismatch.start;
-            for (let k = 0; k < len; k += 1) {
-                const base = seq.charAt(k + mismatch.start);
-                // If softclip length+start is longer than sequence, no need to
-                // continue showing base
-                if (!base) {
-                    return;
-                }
-                const s0 = start + k;
+    const CIGAR = parseCigar(feature.get('CIGAR'));
+    let seqOffset = 0;
+    let refOffset = 0;
+    for (let i = 0; i < CIGAR.length; i += 2) {
+        const op = CIGAR[i + 1];
+        const len = +CIGAR[i];
+        if (op === 'S') {
+            for (let k = 0; k < len; k++) {
+                const base = seq[seqOffset + k];
+                const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx);
                 const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
                 // Black accounts for IUPAC ambiguity code bases such as N that
@@ -39,6 +38,23 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
                     ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }
+            seqOffset += len;
+        }
+        if (op === 'N') {
+            refOffset += len;
+        }
+        if (op === 'M' || op === '=' || op === 'X') {
+            refOffset += len;
+            seqOffset += len;
+        }
+        if (op === 'H') {
+            // do nothing
+        }
+        if (op === 'D') {
+            refOffset += len;
+        }
+        if (op === 'I') {
+            seqOffset += len;
         }
     }
 }

package/esm/SNPCoverageAdapter/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function SNPCoverageAdapterF(pluginManager: PluginManager): void;

package/esm/SNPCoverageAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default function (pluginManager) {
+export default function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'SNPCoverageAdapter',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }