@jbrowse/plugin-alignments 2.11.1 → 2.12.0

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -26,18 +26,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
-const mui_1 = require("tss-react/mui");
 const ui_1 = require("@jbrowse/core/ui");
 const getSAFeatures_1 = require("./getSAFeatures");
 // lazies
 const BreakendOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendOptionDialog'))));
-const useStyles = (0, mui_1.makeStyles)()({
-    cursor: {
-        cursor: 'pointer',
-    },
-});
 function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { view } = model;
     const [res, setRes] = (0, react_1.useState)();
@@ -72,7 +65,7 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
             const [f1, f2] = arg;
             return (react_1.default.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
                 react_1.default.createElement(material_1.Tooltip, { title: "Top panel->Bottom panel" },
-                    react_1.default.createElement(material_1.Link, { href: "#", className: classes.cursor, onClick: event => {
+                    react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
                             event.preventDefault();
                             session.queueDialog(handleClose => [
                                 BreakendOptionDialog,

package/dist/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js

@@ -27,7 +27,7 @@ function SuppAlignmentsLocStrings({ tag, model, }) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
             return (react_1.default.createElement("li", { key: `${locString}-${index}` },
-                react_1.default.createElement(material_1.Link, { onClick: async (event) => {
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: async (event) => {
                         event.preventDefault();
                         // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         (0, util_1.navToLoc)(locString, model);

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -48,13 +61,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

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/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/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -1,18 +1,11 @@
 import React, { lazy, useEffect, useState } from 'react';
 import { Typography, Link, Tooltip } from '@mui/material';
 import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
-import { makeStyles } from 'tss-react/mui';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getSAFeatures } from './getSAFeatures';
 // lazies
 const BreakendOptionDialog = lazy(() => import('./BreakendOptionDialog'));
-const useStyles = makeStyles()({
-    cursor: {
-        cursor: 'pointer',
-    },
-});
 export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const { classes } = useStyles();
     const session = getSession(model);
     const { view } = model;
     const [res, setRes] = useState();
@@ -47,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
             const [f1, f2] = arg;
             return (React.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
                 React.createElement(Tooltip, { title: "Top panel->Bottom panel" },
-                    React.createElement(Link, { href: "#", className: classes.cursor, onClick: event => {
+                    React.createElement(Link, { href: "#", onClick: event => {
                             event.preventDefault();
                             session.queueDialog(handleClose => [
                                 BreakendOptionDialog,

package/esm/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js

@@ -22,7 +22,7 @@ export default function SuppAlignmentsLocStrings({ tag, model, }) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
             return (React.createElement("li", { key: `${locString}-${index}` },
-                React.createElement(Link, { onClick: async (event) => {
+                React.createElement(Link, { href: "#", onClick: async (event) => {
                         event.preventDefault();
                         // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         navToLoc(locString, model);

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -48,13 +61,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

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/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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "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": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }