@jbrowse/plugin-alignments 3.6.4 → 3.7.0

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -18,14 +18,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         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;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;
@@ -68,14 +68,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         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;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;

package/dist/CramAdapter/CramAdapter.js

@@ -220,7 +220,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const chrId = this.refNameToId(refName);
             return chrId !== undefined
                 ? cram.index.getEntriesForRange(chrId, start, end)
-                : [{ sliceBytes: 0 }];
+                : Promise.resolve([{ sliceBytes: 0 }]);
         }));
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,7 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("./util");
-const util_2 = require("../shared/util");
+const readFeaturesToCIGAR_1 = require("./readFeaturesToCIGAR");
+const readFeaturesToMismatches_1 = require("./readFeaturesToMismatches");
+const util_1 = require("../shared/util");
 class CramSlightlyLazyFeature {
     constructor(record, _store) {
         this.record = record;
@@ -67,7 +68,7 @@ class CramSlightlyLazyFeature {
         return this.record.getReadBases();
     }
     get CIGAR() {
-        return (0, util_1.readFeaturesToCIGAR)(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
+        return (0, readFeaturesToCIGAR_1.readFeaturesToCIGAR)(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
     id() {
         return `${this._store.id}-${this.record.uniqueId}`;
@@ -88,7 +89,7 @@ class CramSlightlyLazyFeature {
         return undefined;
     }
     get mismatches() {
-        return (0, util_1.readFeaturesToMismatches)(this.record.readFeatures, this.start, this.qualRaw);
+        return (0, readFeaturesToMismatches_1.readFeaturesToMismatches)(this.record.readFeatures, this.start, this.qualRaw);
     }
     get fields() {
         return {
@@ -119,6 +120,6 @@ class CramSlightlyLazyFeature {
     }
 }
 exports.default = CramSlightlyLazyFeature;
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'fields');
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'CIGAR');
-(0, util_2.cacheGetter)(CramSlightlyLazyFeature, 'mismatches');
+(0, util_1.cacheGetter)(CramSlightlyLazyFeature, 'fields');
+(0, util_1.cacheGetter)(CramSlightlyLazyFeature, 'CIGAR');
+(0, util_1.cacheGetter)(CramSlightlyLazyFeature, 'mismatches');

package/dist/CramAdapter/{util.js → readFeaturesToCIGAR.js}

@@ -2,17 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.readFeaturesToMismatches = readFeaturesToMismatches;
 exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
-function readFeaturesToMismatches(readFeatures, start, qual) {
-    if (!readFeatures) {
-        return [];
-    }
+function readFeaturesToMismatches(readFeatures = [], start, qual) {
     const mismatches = new Array(readFeatures.length);
     let j = 0;
     let insLen = 0;
     let refPos = 0;
     let sublen = 0;
     let lastPos = start;
-    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
+    for (const ret of readFeatures) {
+        const { refPos: p, code, pos, data, sub, ref } = ret;
         sublen = refPos - lastPos;
         lastPos = refPos;
         if (sublen && insLen > 0) {
@@ -20,6 +18,7 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
                 start: refPos,
                 type: 'insertion',
                 base: `${insLen}`,
+                insertedBases: data,
                 length: 0,
             };
             insLen = 0;

package/dist/CramAdapter/readFeaturesToMismatches.d.ts

@@ -0,0 +1,5 @@
+import type { Mismatch } from '../shared/types';
+import type { CramRecord } from '@gmod/cram';
+type ReadFeatures = CramRecord['readFeatures'];
+export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
+export {};

package/dist/CramAdapter/readFeaturesToMismatches.js

@@ -0,0 +1,106 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readFeaturesToMismatches = readFeaturesToMismatches;
+function readFeaturesToMismatches(readFeatures = [], start, qual) {
+    const mismatches = new Array(readFeatures.length);
+    let j = 0;
+    let refPos = 0;
+    let sublen = 0;
+    let lastPos = start;
+    let insertedBases = '';
+    for (const ret of readFeatures) {
+        const { refPos: p, code, pos, data, sub, ref } = ret;
+        sublen = refPos - lastPos;
+        lastPos = refPos;
+        if (sublen && insertedBases.length > 0) {
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${insertedBases.length}`,
+                insertedBases,
+                length: 0,
+            };
+            insertedBases = '';
+        }
+        refPos = p - 1 - start;
+        if (code === 'X') {
+            mismatches[j++] = {
+                start: refPos,
+                length: 1,
+                base: sub,
+                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
+                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
+                type: 'mismatch',
+            };
+        }
+        else if (code === 'I') {
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${data.length}`,
+                insertedBases: data,
+                length: 0,
+            };
+        }
+        else if (code === 'N') {
+            mismatches[j++] = {
+                type: 'skip',
+                length: data,
+                start: refPos,
+                base: 'N',
+            };
+        }
+        else if (code === 'S') {
+            const len = data.length;
+            mismatches[j++] = {
+                start: refPos,
+                type: 'softclip',
+                base: `S${len}`,
+                cliplen: len,
+                length: 1,
+            };
+        }
+        else if (code === 'P') {
+        }
+        else if (code === 'H') {
+            const len = data;
+            mismatches[j++] = {
+                start: refPos,
+                type: 'hardclip',
+                base: `H${len}`,
+                cliplen: len,
+                length: 1,
+            };
+        }
+        else if (code === 'D') {
+            mismatches[j++] = {
+                type: 'deletion',
+                length: data,
+                start: refPos,
+                base: '*',
+            };
+        }
+        else if (code === 'b') {
+        }
+        else if (code === 'q') {
+        }
+        else if (code === 'B') {
+        }
+        else if (code === 'i') {
+            insertedBases += data;
+        }
+        else if (code === 'Q') {
+        }
+    }
+    if (sublen && insertedBases.length > 0) {
+        mismatches[j++] = {
+            start: refPos,
+            type: 'insertion',
+            base: `${insertedBases.length}`,
+            insertedBases,
+            length: 0,
+        };
+        insertedBases = '';
+    }
+    return mismatches.slice(0, j);
+}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -5,13 +5,17 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     resizeHandle: {
         height: 5,
         position: 'absolute',
         zIndex: 2,
+        background: 'transparent',
+        '&:hover': {
+            background: theme.palette.divider,
+        },
     },
-});
+}));
 const AlignmentsDisplay = (0, mobx_react_1.observer)(function AlignmentsDisplay({ model, }) {
     var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;

package/dist/LinearAlignmentsDisplay/model.js

@@ -99,8 +99,9 @@ function stateModelFactory(pluginManager, configSchema) {
             };
         },
         notReady() {
-            return (self.PileupDisplay.renderProps().notReady ||
-                self.SNPCoverageDisplay.renderProps().notReady);
+            var _a, _b;
+            return (((_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.renderProps().notReady) ||
+                ((_b = self.SNPCoverageDisplay) === null || _b === void 0 ? void 0 : _b.renderProps().notReady));
         },
     }))
         .actions(self => ({

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -181,6 +181,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
@@ -195,9 +196,22 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     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;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -206,6 +220,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -54,8 +54,8 @@ const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearP
 const getUniqueTags_1 = require("../shared/getUniqueTags");
 const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
 const ColorByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTagDialog'))));
-const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeightDialog'))));
-const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeightDialog'))));
+const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/SetFeatureHeightDialog'))));
+const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/SetMaxHeightDialog'))));
 const rendererTypes = new Map([
     ['pileup', 'PileupRenderer'],
     ['svg', 'SvgFeatureRenderer'],

package/dist/LinearPileupDisplay/components/GroupByDialog.js

@@ -53,7 +53,7 @@ const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
                                         maxLength: 2,
                                         'data-testid': 'group-tag-name-input',
                                     },
-                                } }), error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { title: "Loading unique tags" })) : tagSet ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Found unique ", tag, " values:"] }), (0, jsx_runtime_1.jsx)("div", { children: tagSet.join(', ') })] })) : null] })) : null] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", disabled: !tagSet, autoFocus: true, onClick: () => {
+                                } }), error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Loading unique tags" })) : tagSet ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Found unique ", tag, " values:"] }), (0, jsx_runtime_1.jsx)("div", { children: tagSet.join(', ') })] })) : null] })) : null] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", disabled: !tagSet, autoFocus: true, onClick: () => {
                             const track = (0, util_1.getContainingTrack)(model);
                             const trackConf = structuredClone((0, mobx_state_tree_1.getSnapshot)(track.configuration));
                             const session = (0, util_1.getSession)(model);
@@ -62,7 +62,7 @@ const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
                                 if (tagSet) {
                                     const ret = [...tagSet, undefined];
                                     for (const tagValue of ret) {
-                                        const t1 = `${trackConf.trackId}-${tag}:${tagValue}-${+Date.now()}-sessionTrack`;
+                                        const t1 = `${trackConf.trackId}-${tag}:${tagValue}-${Date.now()}-sessionTrack`;
                                         session.addTrackConf({
                                             ...trackConf,
                                             trackId: t1,
@@ -90,8 +90,8 @@ const GroupByTagDialog = (0, mobx_react_1.observer)(function (props) {
                                 }
                             }
                             else if (type === 'strand') {
-                                const t1 = `${trackConf.trackId}-${tag}:(-)-${+Date.now()}-sessionTrack`;
-                                const t2 = `${trackConf.trackId}-${tag}:(+)-${+Date.now()}-sessionTrack`;
+                                const t1 = `${trackConf.trackId}-${tag}:(-)-${Date.now()}-sessionTrack`;
+                                const t2 = `${trackConf.trackId}-${tag}:(+)-${Date.now()}-sessionTrack`;
                                 session.addTrackConf({
                                     ...trackConf,
                                     trackId: t1,

package/dist/LinearPileupDisplay/components/SetModificationThresholdDialog.d.ts

@@ -0,0 +1,10 @@
+import type { ColorBy } from '../../shared/types';
+declare const SetModificationThresholdDialog: (props: {
+    model: {
+        modificationThreshold: number;
+        colorBy?: ColorBy;
+        setColorScheme: (colorBy: ColorBy) => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default SetModificationThresholdDialog;

package/dist/LinearPileupDisplay/components/SetModificationThresholdDialog.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const SetModificationThresholdDialog = (0, mobx_react_1.observer)(function (props) {
+    const { model, handleClose } = props;
+    const [threshold, setThreshold] = (0, react_1.useState)(String(model.modificationThreshold));
+    const numThreshold = Number.parseFloat(threshold);
+    const validThreshold = !Number.isNaN(numThreshold) && numThreshold >= 0 && numThreshold <= 100;
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Adjust modification threshold", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Set the minimum probability threshold for displaying modifications" }), (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Only modifications with probability above this threshold will be displayed (0-100%)" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: threshold, onChange: event => {
+                        setThreshold(event.target.value);
+                    }, placeholder: "Enter threshold (e.g., 10)", error: threshold !== '' && !validThreshold, helperText: threshold !== '' && !validThreshold
+                        ? 'Must be a number between 0 and 100'
+                        : '', autoComplete: "off", type: "number", slotProps: {
+                        htmlInput: {
+                            min: 0,
+                            max: 100,
+                            step: 1,
+                        },
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !validThreshold, onClick: () => {
+                                const currentColorBy = model.colorBy || {
+                                    type: 'modifications',
+                                };
+                                model.setColorScheme({
+                                    ...currentColorBy,
+                                    modifications: {
+                                        ...currentColorBy.modifications,
+                                        threshold: numThreshold,
+                                    },
+                                });
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
+});
+exports.default = SetModificationThresholdDialog;

package/dist/LinearPileupDisplay/doAfterAttach.d.ts

@@ -14,6 +14,7 @@ export declare function doAfterAttach(model: {
     setCurrSortBpPerPx: (arg: number) => void;
     setError: (arg: unknown) => void;
     updateVisibleModifications: (arg: ModificationType[]) => void;
+    setSimplexModifications: (arg: string[]) => void;
     setModificationsReady: (arg: boolean) => void;
     setSortReady: (arg: boolean) => void;
     setMessage: (arg: string) => void;

package/dist/LinearPileupDisplay/doAfterAttach.js

@@ -58,13 +58,14 @@ function doAfterAttach(model) {
         }
         const { adapterConfig } = model;
         const { staticBlocks } = (0, util_1.getContainingView)(model);
-        const vals = await (0, getUniqueModifications_1.getUniqueModifications)({
+        const { modifications, simplexModifications } = await (0, getUniqueModifications_1.getUniqueModifications)({
             model,
             adapterConfig,
             blocks: staticBlocks,
         });
         if ((0, mobx_state_tree_1.isAlive)(model)) {
-            model.updateVisibleModifications(vals);
+            model.updateVisibleModifications(modifications);
+            model.setSimplexModifications(simplexModifications);
             model.setModificationsReady(true);
         }
     }, { delay: 1000 });

package/dist/LinearPileupDisplay/model.d.ts

@@ -186,6 +186,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -200,9 +201,22 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     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;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -211,6 +225,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -306,10 +321,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     sortReady: boolean;
     currSortBpPerPx: number;
     visibleModifications: import("mobx").ObservableMap<string, ModificationTypeWithColor>;
+    simplexModifications: Set<string>;
     modificationsReady: boolean;
 } & {
     setCurrSortBpPerPx(n: number): void;
     updateVisibleModifications(uniqueModifications: ModificationType[]): void;
+    setSimplexModifications(simplex: string[]): void;
     setModificationsReady(flag: boolean): void;
     setSortReady(flag: boolean): void;
     clearSelected(): void;
@@ -321,6 +338,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     reload(): void;
 } & {
     readonly visibleModificationTypes: string[];
+    readonly modificationThreshold: any;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {

package/dist/LinearPileupDisplay/model.js

@@ -46,9 +46,11 @@ 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 modificationData_1 = require("../shared/modificationData");
 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'))));
+const SetModificationThresholdDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetModificationThresholdDialog'))));
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearPileupDisplay', (0, SharedLinearPileupDisplayMixin_1.SharedLinearPileupDisplayMixin)(configSchema), mobx_state_tree_1.types.model({
@@ -62,6 +64,7 @@ function stateModelFactory(configSchema) {
         sortReady: false,
         currSortBpPerPx: 0,
         visibleModifications: mobx_1.observable.map({}),
+        simplexModifications: new Set(),
         modificationsReady: false,
     }))
         .actions(self => ({
@@ -78,6 +81,11 @@ function stateModelFactory(configSchema) {
                 }
             }
         },
+        setSimplexModifications(simplex) {
+            for (const entry of simplex) {
+                self.simplexModifications.add(entry);
+            }
+        },
         setModificationsReady(flag) {
             self.modificationsReady = flag;
         },
@@ -130,6 +138,10 @@ function stateModelFactory(configSchema) {
         get visibleModificationTypes() {
             return [...self.visibleModifications.keys()];
         },
+        get modificationThreshold() {
+            var _a, _b, _c;
+            return (_c = (_b = (_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.modifications) === null || _b === void 0 ? void 0 : _b.threshold) !== null && _c !== void 0 ? _c : 10;
+        },
         get rendererConfig() {
             const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, hideSmallIndels, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
@@ -163,13 +175,14 @@ function stateModelFactory(configSchema) {
         const { trackMenuItems: superTrackMenuItems, renderPropsPre: superRenderPropsPre, renderProps: superRenderProps, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
         return {
             renderPropsPre() {
-                const { sortedBy, showSoftClipping, visibleModifications } = self;
+                const { sortedBy, showSoftClipping, visibleModifications, simplexModifications, } = self;
                 const superProps = superRenderPropsPre();
                 return {
                     ...superProps,
                     showSoftClip: showSoftClipping,
                     sortedBy,
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
+                    simplexModifications: [...simplexModifications],
                 };
             },
             renderProps() {
@@ -232,22 +245,26 @@ function stateModelFactory(configSchema) {
                                 subMenu: self.modificationsReady
                                     ? [
                                         {
-                                            label: 'All modifications',
+                                            label: `All modifications (>= ${self.modificationThreshold}% prob)`,
                                             onClick: () => {
                                                 self.setColorScheme({
                                                     type: 'modifications',
+                                                    modifications: {
+                                                        threshold: self.modificationThreshold,
+                                                    },
                                                 });
                                             },
                                         },
                                         ...self.visibleModificationTypes.map(key => {
                                             var _a;
                                             return ({
-                                                label: `Show only ${((_a = util_2.modificationData[key]) === null || _a === void 0 ? void 0 : _a.name) || key}`,
+                                                label: `Show only ${((_a = modificationData_1.modificationData[key]) === null || _a === void 0 ? void 0 : _a.name) || key}  (>= ${self.modificationThreshold}% prob)`,
                                                 onClick: () => {
                                                     self.setColorScheme({
                                                         type: 'modifications',
                                                         modifications: {
                                                             isolatedModification: key,
+                                                            threshold: self.modificationThreshold,
                                                         },
                                                     });
                                                 },
@@ -261,6 +278,7 @@ function stateModelFactory(configSchema) {
                                                     type: 'modifications',
                                                     modifications: {
                                                         twoColor: true,
+                                                        threshold: self.modificationThreshold,
                                                     },
                                                 });
                                             },
@@ -268,13 +286,14 @@ function stateModelFactory(configSchema) {
                                         ...self.visibleModificationTypes.map(key => {
                                             var _a;
                                             return ({
-                                                label: `Show only ${((_a = util_2.modificationData[key]) === null || _a === void 0 ? void 0 : _a.name) || key} (<50% prob colored blue)`,
+                                                label: `Show only ${((_a = modificationData_1.modificationData[key]) === null || _a === void 0 ? void 0 : _a.name) || key} (<50% prob colored blue)`,
                                                 onClick: () => {
                                                     self.setColorScheme({
                                                         type: 'modifications',
                                                         modifications: {
                                                             isolatedModification: key,
                                                             twoColor: true,
+                                                            threshold: self.modificationThreshold,
                                                         },
                                                     });
                                                 },
@@ -286,9 +305,25 @@ function stateModelFactory(configSchema) {
                                             onClick: () => {
                                                 self.setColorScheme({
                                                     type: 'methylation',
+                                                    modifications: {
+                                                        threshold: self.modificationThreshold,
+                                                    },
                                                 });
                                             },
                                         },
+                                        { type: 'divider' },
+                                        {
+                                            label: `Adjust threshold (${self.modificationThreshold}%)`,
+                                            onClick: () => {
+                                                (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                                    SetModificationThresholdDialog,
+                                                    {
+                                                        model: self,
+                                                        handleClose,
+                                                    },
+                                                ]);
+                                            },
+                                        },
                                     ]
                                     : [
                                         {

package/dist/LinearReadArcsDisplay/index.js

@@ -46,7 +46,7 @@ function register(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearReadArcsDisplay',
-            displayName: 'Arc display',
+            displayName: 'Read arc display',
             configSchema,
             stateModel: (0, model_1.default)(configSchema),
             trackType: 'AlignmentsTrack',